Miracle-dz/UniFAR-FTUs huggingface dataset:
Probabilistic Graphical Models for Dynamic PET: A Novel Approach to Direct Parametric Map Estimation and Image Reconstruction

In the context of dynamic emission tomography, the conventional processing pipeline consists of independent image reconstruction of single-time frames, followed by the application of a suitable kinetic model to time-activity curves (TACs) at the voxel or region-of-interest level. Direct 4D positron emission tomography (PET) reconstruction, by contrast, seeks to move beyond this scheme and incorporate information from multiple time frames within the reconstruction task. Established direct methods are based on a deterministic description of voxelwise TACs, captured by the chosen kinetic model, considering the photon counting process the only source of uncertainty. In this paper, we introduce a new probabilistic modeling strategy based on the key assumption that activity time course would be subject to uncertainty even if the parameters of the underlying dynamic process are known. This leads to a hierarchical model that we formulate using the formalism of probabilistic graphical modeling. The inference is addressed using a new iterative algorithm, in which kinetic modeling results are treated as prior expectation of activity time course, rather than as a deterministic match, making it possible to control the trade-off between a data-driven and a model-driven reconstruction. The proposed method is flexible to an arbitrary choice of (linear and nonlinear) kinetic models, it enables the inclusion of arbitrary (sub)differentiable priors for parametric maps, and it is simple to implement. Computer simulations and an application to a real-patient scan show how the proposed method is able to generalize over conventional indirect and direct approaches, providing a bridge between them by properly tuning the impact of the kinetic modeling step on image reconstruction.
CoNDA: Efficient Cache Coherence Support for Near-Data Accelerators

Specialized on-chip accelerators are widely used to improve the energy efficiency of computing systems. Recent advances in memory technology have enabled near-data accelerators (NDAs), which reside off-chip close to main memory and can yield further benefits than on-chip accelerators. However, enforcing coherence with the rest of the system, which is already a major challenge for accelerators, becomes more difficult for NDAs. This is because (1) the cost of communication between NDAs and CPUs is high, and (2) NDA applications generate a lot of off-chip data movement. As a result, as we show in this work, existing coherence mechanisms eliminate most of the benefits of NDAs. We extensively analyze these mechanisms, and observe that (1) the majority of off-chip coherence traffic is unnecessary, and (2) much of the off-chip traffic can be eliminated if a coherence mechanism has insight into the memory accesses performed by the NDA. Based on our observations, we propose CoNDA, a coherence mechanism that lets an NDA optimistically execute an NDA kernel, under the assumption that the NDA has all necessary coherence permissions. This optimistic execution allows CoNDA to gather information on the memory accesses performed by the NDA and by the rest of the system. CoNDA exploits this information to avoid performing unnecessary coherence requests, and thus, significantly reduces data movement for coherence. We evaluate CoNDA using state-of-the-art graph processing and hybrid in-memory database workloads. Averaged across all of our workloads operating on modest data set sizes, CoNDA improves performance by 19.6% over the highest-performance prior coherence mechanism (66.0%/51.7% over a CPU-only/NDA-only system) and reduces memory system energy consumption by 18.0% over the most energy-efficient prior coherence mechanism (43.7% over CPU- only). CoNDA comes within 10.4% and 4.4% of the performance and energy of an ideal mechanism with no cost for coherence. The benefits of CoNDA increase with large data sets, as CoNDA improves performance over the highest-performance prior coherence mechanism by 38.3% (8.4x/7.7x over CPU-only/NDA-only), and comes within 10.2% of an ideal no-cost coherence mechanism.
Accuracy of the Low-Dose ACTH Stimulation Test for Adrenal Insufficiency Diagnosis: A Re-Assessment of the Cut-Off Value

Background: The clinical practice shows that many low-dose ACTH-stimulation tests have a false positive result. The aim of the study was to determine the diagnostic accuracy of a low-dose ACTH-stimulation test in the diagnosis of adrenal insufficiency and to define its optimal cut-off. Methods: We analyzed data from 103 patients undergoing 1 µg ACTH-stimulation test. Four patients had adrenal insufficiency (AI) upon follow up: Two primary, and two secondary AI. Cortisol serum levels were evaluated at time 0, 20’, and 30’ after the injection of 1 µg i.v. of ACTH. The sensitivity, specificity, accuracy, and positive and negative predictive values of the test were calculated for both 20’ and 30’ sampling. The receiver operating characteristic (ROC) curve was obtained to assess the sensitivity and specificity of low-dose ACTH-stimulation test in the diagnosis of adrenal insufficiency at different cut-off values. Results: Considering 500 nmol/L as the standard cut-off value, low-dose ACTH stimulation test showed a 100% sensitivity and a 67.3% specificity, with a high rate of false positive results. ROC curve analysis showed that the cut-off of 401.5 nmol/L is the best compromise between sensitivity (100%) and specificity (93.9%). Conclusions: By using a cut-off value of 401.5 nmol/L for the low-dose ACTH stimulation test, the number of false positive patients decreased significantly, but the sensitivity remained high.
Design and construction of cost-effective tapered amplifier systems for laser cooling and trapping experiments

We present plans for the construction and operation of a tapered optical amplifier (TA) system seeded by a single-mode, frequency-tunable, near-IR external-cavity diode laser. Our plans include machine drawings for the parts, electronic circuit diagrams, and information on prices and vendors. Instructions are provided on how to safely couple light into and out of the TA chip. Practical aspects of handling the chip are discussed as well. Because many cold atom experiments require light beams with Gaussian spatial profiles, measurements of the tapered amplifier light output through a single-mode optical fiber are presented as a function of seed intensity, polarization, and driving current.
A Fully Reconfigurable Polarimetric Phased Array Antenna Testbed

The configurable phased array demonstrator (CPAD) is a low-cost, reconfigurable, small-scale testbed for the dual-polarized array antenna and radar prototype. It is based on the concept that individual transmit and receive (TR) modules and radiating elements can be configured in different ways to study the impact of various array manifolds on radiation pattern performance. For example, CPAD is configured as (a) a 4 × 4 planar array, (b) a planar array with mirror configuration, and (c) a circular array to support the multifunctional phased array radar (MPAR) system risk reduction studies. System descriptions are given in detail, and measurements are made and results are analyzed.
Hybrid bag of approaches to characterize selection criteria for cohort identification

OBJECTIVE The 2018 National NLP Clinical Challenge (2018 n2c2) focused on the task of cohort selection for clinical trials, where participating systems were tasked with analyzing longitudinal patient records to determine if the patients met or did not meet any of the 13 selection criteria. This article describes our participation in this shared task. MATERIALS AND METHODS We followed a hybrid approach combining pattern-based, knowledge-intensive, and feature weighting techniques. After preprocessing the notes using publicly available natural language processing tools, we developed individual criterion-specific components that relied on collecting knowledge resources relevant for these criteria and pattern-based and weighting approaches to identify "met" and "not met" cases. RESULTS As part of the 2018 n2c2 challenge, 3 runs were submitted. The overall micro-averaged F1 on the training set was 0.9444. On the test set, the micro-averaged F1 for the 3 submitted runs were 0.9075, 0.9065, and 0.9056. The best run was placed second in the overall challenge and all 3 runs were statistically similar to the top-ranked system. A reimplemented system achieved the best overall F1 of 0.9111 on the test set. DISCUSSION We highlight the need for a focused resource-intensive effort to address the class imbalance in the cohort selection identification task. CONCLUSION Our hybrid approach was able to identify all selection criteria with high F1 performance on both training and test sets. Based on our participation in the 2018 n2c2 task, we conclude that there is merit in continuing a focused criterion-specific analysis and developing appropriate knowledge resources to build a quality cohort selection system.
Predicting biomedical relationships using the knowledge and graph embedding cascade model

Advances in machine learning and deep learning methods, together with the increasing availability of large-scale pharmacological, genomic, and chemical datasets, have created opportunities for identifying potentially useful relationships within biochemical networks. Knowledge embedding models have been found to have value in detecting knowledge-based correlations among entities, but little effort has been made to apply them to networks of biochemical entities. This is because such networks tend to be unbalanced and sparse, and knowledge embedding models do not work well on them. However, to some extent, the shortcomings of knowledge embedding models can be compensated for if they are used in association with graph embedding. In this paper, we combine knowledge embedding and graph embedding to represent biochemical entities and their relations as dense and low-dimensional vectors. We build a cascade learning framework which incorporates semantic features from the knowledge embedding model, and graph features from the graph embedding model, to score the probability of linking. The proposed method performs noticeably better than the models with which it is compared. It predicted links and entities with an accuracy of 93%, and its average hits@10 score has an average of 8.6% absolute improvement compared with original knowledge embedding model, 1.1% to 9.7% absolute improvement compared with other knowledge and graph embedding algorithm. In addition, we designed a meta-path algorithm to detect path relations in the biomedical network. Case studies further verify the value of the proposed model in finding potential relationships between diseases, drugs, genes, treatments, etc. Amongst the findings of the proposed model are the suggestion that VDR (vitamin D receptor) may be linked to prostate cancer. This is backed by evidence from medical databases and published research, supporting the suggestion that our proposed model could be of value to biomedical researchers.
Disentangling the effects of foliar vs. floral herbivory of leaf-cutting ants on the plant reproductive success of Miconia nervosa (Smith) Triana (Family Melastomataceae)

Abstract Flower and leaf herbivory might cause relevant and negative impacts on plant fitness. While flower removal or damage by florivores produces direct negative effects on plant fitness, folivores affect plant fitness by reducing resource allocation to reproduction. In this study, we examine the effects of both flower and leaf herbivory by leaf-cutting ants on the reproductive success of the shrub species Miconia nervosa (Smith) Triana (Family Melastomataceae) in a fragment of Atlantic Forest in Northeast Brazil. We conducted a randomized block-designed field experiment with nine replicates (blocks), in which three plants per block were assigned to one of the three following treatments: undamaged plants (ant exclusion), leaf-damaged plants (ant exclusion from reproductive organs, but not from leaves), and flower + leaf-damaged plants (no exclusion of ants). We then measured flower production, fruit set, and fruit production. Our results showed that flower + leaf-damaged plants reduced flower production nearly twofold in relation to undamaged plants, while flower set in leaf-damaged plants remained constant. The number of flowers that turned into fruits (i.e., fruit set), however, increased by 15% in flower + leaf-damaged plants, while it slightly decreased in leaf-damaged compared to undamaged plants. Contrastingly, fruit production was similar between all treatments. Taken together, our results suggest a prominent role of ant floral herbivory across different stages of the reproductive cycle in M. nervosa, with no consequences on final fruit production. The tolerance of M. nervosa to leaf-cutting ant herbivory might explain its high abundance in human-modified landscapes where leaf-cutting ants are hyper-abundant.
Clinical practice guideline on peri- and postoperative care of arteriovenous fistulas and grafts for haemodialysis in adults.

Int J Clin Pract 2010; 64: 1239–1244 94. Kaufman JS, Connor TZ, Zhang JH et al. Randomized controlled trial of clopidogrel plus aspirin to prevent hemodialysis access graft thrombosis. J Am Soc Nephrol 2003; 14: 2313–2321 95. Kooistra MP, van Es A, Marx JJ et al. Low-dose aspirin does not prevent thrombovascular accidents in low-risk haemodialysis patients during treatment with recombinant human erythropoietin. Nephrol Dial Transplant
Performance analysis of space-shift keying over negative-exponential and log-normal FSO channels

The average bit-error rate (ABER) performance of free-space optical (FSO) communication links is investigated for space-shift keying (SSK) over log-normal and negative-exponential atmospheric turbulence channels. SSK is compared with repetition codes and a single-input single-output system using multiple pulse amplitude modulations. Simulation results show that the signal-to-noise ratio gain of SSK largely increases with greater spectral efficiencies and/or higher turbulence effects. A tight bound for ABER is derived based on an exact moment generation function (MGF) for negative-exponential channel and an approximate MGF for log-normal channel. Finally, extensive Monte Carlo simulations are run to validate the analytical analysis.
Light, canopy closure, and overstory retention in upland Ozark forests

Foresters, wildlife biologists, and naturalists manipulate forest composition and structure for numerous reasons including forest regeneration, timber production, wildlife habitat, conservation of native biodiversity, and ecosystem restoration. Light conditions in the understory of forests and woodlands are often key in meeting the management objectives. In this study, predictive models were developed relating mean diurnal understory photosynthetically active radiation (PAR) (400 to 700 nm) as percentages of above canopy (understory PAR) to measures of canopy closure, stocking, basal area, and density. Relationships between percent crown closure and density in Missouri’s upland oak (Quercus spp.) and oak-pine (Pinus spp.) stands are not well defined, nor are the relationships between each measure and light conditions near the forest floor. Our objectives for this paper were: (1) to analyze the relationships between understory PAR and stand metrics and (2) to analyze the relationships between canopy closure and stand metrics. Understory PAR may be predicted by models utilizing stocking, basal area, or stand density, but understory PAR was primarily controlled by canopy closure. Canopy closure was related to stocking and density.
Design of a frequency control system in a microgrid containing HVAC

The advent of smart grids and the growing procedure of controllable loads and tending to the demand response (DR) in small power systems have helped with new ideas, which can be used in the frequency stability of a microgrid. This paper presents a novel model for frequency control of a microgrid containing controllable load and renewable resources. The controllable loads used in this paper are such as heating, ventilation, and air conditioning, which change temperature based on frequency change. The microgrid is hybrid (AC/DC) and able to connect to and energy exchange with the utility grid. The design of PID controller parameters is considered an optimization problem according to the time domain-based objective function solved by the particle swarm optimization (PSO) algorithm, which has a strong ability tond the most optimistic results. The effectiveness and robustness of the proposed controller are demonstrated through nonlinear time-domain simulation. Finally, for the simulation and analysis, the output results have been presented and studied.
Rituximab-CHOP Consortium Program demonstrates high-risk gene expression signatures : a report from The activated B-cell subtype of diffuse large B-cell lymphoma and MYC / BCL 2 protein coexpression contributes to the inferior survival of

Chen, Ronald S. Go, Miguel A. Piris, Michael B. Møller, L. Jeffrey Medeiros and Ken H. Young J. M. Ferreri, Fan Zhou, Graham W. Slack, Randy D. Gascoyne, Meifeng Tu, Daina Variakojis, Weina Xiaoying Zhao, J. Han van Krieken, Qin Huang, Jooryung Huh, Weiyun Ai, Maurilio Ponzoni, Andrés April Chiu, Attilio Orazi, Youli Zu, Govind Bhagat, Kristy L. Richards, Eric D. Hsi, William W. L. Choi, Wei-min Liu, Carlo Visco, Yong Li, Roberto N. Miranda, Santiago Montes-Moreno, Karen Dybkaer, Shimin Hu, Zijun Y. Xu-Monette, Alexander Tzankov, Tina Green, Lin Wu, Aarthi Balasubramanyam, International DLBCL Rituximab-CHOP Consortium Program demonstrates high-risk gene expression signatures: a report from The activated B-cell subtype of diffuse large B-cell lymphoma and MYC/BCL2 protein coexpression contributes to the inferior survival of
Parkin Mutation Affects Clock Gene-Dependent Energy Metabolism

Growing evidence highlights a tight connection between circadian rhythms, molecular clockworks, and mitochondrial function. In particular, mitochondrial quality control and bioenergetics have been proven to undergo circadian oscillations driven by core clock genes. Parkinson’s disease (PD) is a chronic neurodegenerative disease characterized by a selective loss of dopaminergic neurons. Almost half of the autosomal recessive forms of juvenile parkinsonism have been associated with mutations in the PARK2 gene coding for parkin, shown to be involved in mitophagy-mediated mitochondrial quality control. The aim of this study was to investigate, in fibroblasts from genetic PD patients carrying parkin mutations, the interplay between mitochondrial bioenergetics and the cell autonomous circadian clock. Using two different in vitro synchronization protocols, we demonstrated that normal fibroblasts displayed rhythmic oscillations of both mitochondrial respiration and glycolytic activity. Conversely, in fibroblasts obtained from PD patients, a severe damping of the bioenergetic oscillatory patterns was observed. Analysis of the core clock genes showed deregulation of their expression patterns in PD fibroblasts, which was confirmed in induced pluripotent stem cells (iPSCs) and induced neural stem cells (iNSCs) derived thereof. The results from this study support a reciprocal interplay between the clockwork machinery and mitochondrial energy metabolism, point to a parkin-dependent mechanism of regulation, and unveil a hitherto unappreciated level of complexity in the pathophysiology of PD and eventually other neurodegenerative diseases.
Models for Optimising Dynamic Urban Mobility (MODUM)

MODUM (Models for Optimising Dynamic Urban Mobility) is a European Commission 7th Framework (FP7) project that aims to develop a new optimisation approach to traffic management, capable of dynamically adapting the overall flows of traffic to unexpected disturbances to minimise carbon emissions within an urban complex environment. In particular, MODUM employs the multi-agent system paradigm, which is used in a novel setting, i.e., for distributed coordination and forecasting (of, e.g., travel times) by means of self-organising virtual ants. In addition, multi-modal solutions are provided through a noticeboard and bidding approach using real-time data and declared destinations. The system syntheses both approaches into a single integrated model, incorporating the many telecommunication challenges of a realistic demonstrator. As there are many components in the system, we also provide an evaluation and validation framework that asserts that the software is of high quality, the traffic models are verified to reproduce realistic phenomena, and the definition of parameters and indicators for setting up and carrying out field trials. These take place in the cities of Nottingham (United Kingdom) and Sofia (Bulgary). There, a series of simulation experiments of realistic complexity are constructed using historical and real-time data feeds available from available transport sensing infrastructure.
A comparison of the nutritive value of organically and conventionally grown barley and wheat crops

The objective of this study was to investigate if there is any significant difference in yield and nutri- tive value between organically and conventionally grown wheat and barley crops. Each cultivation system was carried out in three plots of each crop bordering each other to assure similar soil properties. Both crops were harvested in May at post-bloom stage, and the whole plan ts were used for the analyses. The true in vitro digestibility of dry matter (IVDMD) and neutral-detergent fi