Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-dimensional Medical Image Segmentation with Partial Volume and Gradient Modelling

We present a new algorithm for the feature-space based segmentation of medical image volumes, based on a unified mathematical framework that incorporates both intensity and local gradient information. The algorithm addresses the problem of partial volume tissue estimation and is capable of using multiple image volumes, and the associated multi-dimensional image gradient, to increase tissue separability. Clustering is performed in the combined intensity and gradient histogram, followed by the use of Bayes theory to generate probability maps showing the most likely tissue volume fractions within each voxel, rather than a classification to a single tissue type. The approach also supports reconstruction of images from the estimates of volumetric voxel contents and the tissue model parameters. Evaluation of the algorithm comprised three stages. First, objective measurements of segmentation accuracy, and the increase in accuracy when local gradient information was included in the feature space, were produced using simulated magnetic resonance (MR) images of the normal brain. Second, application to clinical MR data was demonstrated using an exemplar medical problem, the measurement of cerebrospinal fluid (CSF) volume in 70 normal volunteers, through comparison to a “bronze-standard” consisting of previously published measurements. Third, the accuracy of the multidimensional approach was demonstrated by assessing the errors on reconstructed images produced from the segmentation result. We conclude that the inclusion of gradient information in the feature space can result in significant improvements in segmentation accuracy compared to the use of intensity information alone.
Impact of the Atlantic Multidecadal Oscillation on Baltic Sea Variability

The Atlantic Multidecadal Oscillation (AMO) is a natural mode of variability of the North Atlantic sea surface temperature. The AMO can be used to describe the complex interaction of the coupled atmosphere‐ocean system of the North Atlantic. By analyzing a preindustrial period of 850 years with a regional climate model, we show that the AMO influences the Baltic Sea. AMO‐related changes of the atmospheric circulation affect precipitation over the Baltic Sea region, which leads to altered river runoff influencing the salinity of the Baltic Sea. A wavelet coherence analysis reveals a persistent coherence between AMO and salinity for the whole period of 850 years. This suggests that the Baltic Sea is under the constant influence of the AMO. Our results provide strong evidence for long‐term changes in the Baltic Sea as a result of changing AMO phases.
Exploring Algorithmic Options for the Efficient Design and Reconfiguration of Reactive Robot Swarms

A key challenge in robot swarm engineering is the design of individual robot controllers such that the robots as a group can perform a specified task. In this paper, we explore algorithmic options for designing and reconfiguring swarms of synchronous reactive robots to perform a joint navigation / morphogenesis task in a known world. Our results show that neither of these problems can be solved both efficiently and correctly either in general or relative to a surprisingly large number of restrictions on robot and swarm architecture. We also give restrictions under which these problems can be solved both efficiently and correctly.A key challenge in robot swarm engineering is the design of individual robot controllers such that the robots as a group can perform a specified task. In this paper, we explore algorithmic options for designing and reconfiguring swarms of synchronous reactive robots to perform a joint navigation / morphogenesis task in a known world. Our results show that neither of these problems can be solved both efficiently and correctly either in general or relative to a surprisingly large number of restrictions on robot and swarm architecture. We also give restrictions under which these problems can be solved both efficiently and correctly.
Nonperturbative infrared fixed point in sextet QCD

The SU(3) gauge theory with fermions in the sextet representation is one of several theories of interest for technicolor models. We have carried out a Schrodinger functional (SF) calculation for the lattice theory with two flavors of Wilson fermions. We find that the discrete beta function changes sign when the SF renormalized coupling is in the neighborhood of g^2 = 2.0, showing a breakdown of the perturbative picture even though the coupling is weak. The most straightforward interpretation is an infrared-stable fixed point.
Do we know how much fluvial sediment reaches the sea? Decreased river monitoring of U.S. coastal rivers

Given the present and future changing climate and human changes to land use and river control, river sediment fluxes to coastal systems are changing and will continue to change in the future. To delineate these changes and their effects, it is increasingly important to document the fluxes of river‐borne sediment discharged to the sea. Unfortunately, broad‐scale river sediment monitoring programs established more than 50 years ago in the United States have diminished substantially and now focus principally on the largest rivers and estuaries. Unless addressed, these data gaps will provide significant challenges in addressing fundamental scientific and management questions about the effects of climate change and sea‐level rise in our estuaries and on our coasts. Water quality sampling has been conducted on American rivers for well over 100 years. Early sampling of water quality was in large part done to certify the potability of local drinking waters (e.g., Dole & Stabler, 1909), and suspended‐sediment concentrations were measured in addition to dissolved and particulate species. These measurements allowed for the calculation of suspended‐sediment discharge and thereby led to estimates of landscape denudation (e.g., Dole & Stabler, 1909). Expansion of river suspended‐sediment sampling in the mid and later parts of the 20th century allowed scientists and planners to estimate the effects of deforestation, farming, construction, urbanization, and dam building on the fluxes of sediment (e.g., Curtis, Culbertson, & Chase, 1973; Meade, 1988; Milliman & Farnsworth, 2011; Wolman & Schick, 1967). In recent decades, new management challenges, including regulation of river flows, restoration of fluvial and coastal habitats, new or persistent water quality problems, and even the deconstruction of dams—all in the face of a changing climate and continual modification of watershed landscapes—have required detailed measurements of river sediment discharge (e.g., Magirl et al., 2015; Topping et al., 2010). Additional challenges exist along our coasts, where shoreline erosion and coastal flooding will increase with future climate change and
ION CHANNELS , RECEPTORS AND TRANSPORTERS Sodium channelopathies and pain

Chronic pain often represents a severe, debilitating condition. Up to 10% of the worldwide population are affected, and many patients are poorly responsive to current treatment strategies. Nociceptors detect noxious conditions to produce the sensation of pain, and this signal is conveyed to the CNS by means of action potentials. The fast upstroke of action potentials is mediated by voltage-gated sodium channels, of which nine pore-forming α-subunits (Nav1.1– 1.9) have been identified. Heterogeneous functional properties and distinct expression patterns denote specialized functions of each subunit. The Nav1.7 and Nav1.8 subunits have emerged as key molecules involved in peripheral pain processing and in the development of an increased pain sensitivity associated with inflammation and tissue injury. Several mutations in the SCN9A gene encoding for Nav1.7 have been identified as important cellular substrates for different heritable pain syndromes. This review aims to cover recent progress on our understanding of how biophysical properties of mutant Nav1.7 translate into an aberrant electrogenesis of nociceptors. We also recapitulate the role of Nav1.8 for peripheral pain processing and of additional sodium channelopathies which have been linked to disorders with pain as a significant component.
Diagnostic and Prognostic Significance of the CFU-c Assay in Acute Nonlymphoblastic Leukemia 1

A simplified system for classification of aggregate incidence and growth pattern in the CFU-c (colony-forming units in cul ture) assay, allowing simple and reproducible interpretation of test results, was developed and applied to 552 bone marrow samples from 202 adult patients with acute leukemia. Ninetysix consecutive patients with acute nonlymphoblastic leukemia were studied at diagnosis. The microcluster growth pattern ("acute myeloid leukemia-type") found in 57% of the patients, was significantly associated with higher remission induction rates on both protocols (p = 0.004). No relationship between growth pattern at diagnosis and remission duration was ob served. The acute myeloid leukemia-type growth pattern was found to be more frequent in leukemias exhibiting morpholog ical evidence for partial myeloid or monocytic differentiation. The favorable prognostic significance of Auer rods previously described was recognized in two CFU-c growth pattern cate gories. Of patients exhibiting an acute myeloid leukemiagrowth pattern and Auer rods, 89% obtained complete remis sions compared to 38% in the Auer rod-negative group showing other growth pattern variants. The CFU-c assays performed during complete remission on 354 samples of 48 patients with acute nonlymphoblastic leukemia and, as a control, on 85 samples of 43 patients with acute lymphoblastic leukemia revealed marked spontaneous as well as chemotherapy-related fluctuations of aggregate incidence and growth pattern. These and similar observations obtained with other assay systems are probably of major pathophysiological significance but preclude clinical application of the CFU-c assay to the monitoring of remission status in patients with acute nonlymphoblastic leu kemia.
CD4+ T-cell anergy induced by lin− CD117(c-kit)+ stem cell-derived immature dendritic cells loaded with nuclear antigen derived from Trypanosoma equiperdum

Dendritic cells (DCs) are professional antigen-presenting cells, which have the extraordinary capacity to initiate naïve T-cell-mediated primary immune responses. To investigate the role of DCs in the induction of antigen-specific tolerance, the immature DCs (imDCs) and mature DCs (mDCs) were generated in vitro from lin− CD117(c-kit)+ stem cells isolated from mice bone marrow. Flow cytometry and confocal microscopy were used to characterize the phenotypes of DCs. These cells were loaded with nuclear antigen derived from Trypanosoma equiperdum and then co-cultured with naïve CD4+ T cells. It was found that imDC-treated T cells had lower proliferation level and cytokine expression of interleukin (IL)-2, IL-4, IL-12, and interferon-γ compared with mDC-treated T cells. These results demonstrated that the maturation status of DCs is critical for preventing the production of autoantibodies.
Multi-execution: multicore caching for data-similar executions

While microprocessor designers turn to multicore architectures to sustain performance expectations, the dramatic increase in parallelism of such architectures will put substantial demands on off-chip bandwidth and make the memory wall more significant than ever. This paper demonstrates that one profitable application of multicore processors is the execution of many similar instantiations of the same program. We identify that this model of execution is used in several practical scenarios and term it as "multi-execution. " Often, each such instance utilizes very similar data. In conventional cache hierarchies, each instance would cache its own data independently. We propose the Mergeable cache architecture that detects data similarities and merges cache blocks, resulting in substantial savings in cache storage requirements. This leads to reductions in off-chip memory accesses and overall power usage, and increases in application performance. We present cycle-accurate simulation results of 8 benchmarks (6 from SPEC2000) to demonstrate that our technique provides a scalable solution and leads to significant speedups due to reductions in main memory accesses. For 8 cores running 8 similar executions of the same application and sharing an exclusive 4-MB, 8-way L2 cache, the Mergeable cache shows a speedup in execution by 2.5x on average (ranging from 0.93x to 6.92x), while posing an overhead of only 4.28% on cache area and 5.21% on power when it is used.
Multivariate Modeling Identifies Neutrophil- and Th17-Related Factors as Differential Serum Biomarkers of Chronic Murine Colitis

Background Diagnosis of chronic intestinal inflammation, which characterizes inflammatory bowel disease (IBD), along with prediction of disease state is hindered by the availability of predictive serum biomarker. Serum biomarkers predictive of disease state will improve trials for therapeutic intervention, and disease monitoring, particularly in genetically susceptible individuals. Chronic inflammation during IBD is considered distinct from infectious intestinal inflammation thereby requiring biomarkers to provide differential diagnosis. To address whether differential serum biomarkers could be identified in murine models of colitis, immunological profiles from both chronic spontaneous and acute infectious colitis were compared and predictive serum biomarkers identified via multivariate modeling. Methodology/Principal Findings Discriminatory multivariate modeling of 23 cytokines plus chlorotyrosine and nitrotyrosine (protein adducts from reactive nitrogen species and hypochlorite) in serum and tissue from two murine models of colitis was performed to identify disease-associated biomarkers. Acute C. rodentium-induced colitis in C57BL/6J mice and chronic spontaneous Helicobacter-dependent colitis in TLR4−/− x IL-10−/− mice were utilized for evaluation. Colon profiles of both colitis models were nearly identical with chemokines, neutrophil- and Th17-related factors highly associated with intestinal disease. In acute colitis, discriminatory disease-associated serum factors were not those identified in the colon. In contrast, the discriminatory predictive serum factors for chronic colitis were neutrophil- and Th17-related factors (KC, IL-12/23p40, IL-17, G-CSF, and chlorotyrosine) that were also elevated in colon tissue. Chronic colitis serum biomarkers were specific to chronic colitis as they were not discriminatory for acute colitis. Conclusions/Significance Immunological profiling revealed strikingly similar colon profiles, yet distinctly different serum profiles for acute and chronic colitis. Neutrophil- and Th17-related factors were identified as predictive serum biomarkers of chronic colitis, but not acute colitis, despite their presence in colitic tissue of both diseases thereby demonstrating the utility of mathematical modeling for identifying disease-associated serum biomarkers.
Autophagic Killing Effects against Mycobacterium tuberculosis by Alveolar Macrophages from Young and Aged Rhesus Macaques

Non-human primates, notably rhesus macaques (Macaca mulatta, RM), provide a robust experimental model to investigate the immune response to and effective control of Mycobacterium tuberculosis infections. Changes in the function of immune cells and immunosenescence may contribute to the increased susceptibility of the elderly to tuberculosis. The goal of this study was to examine the impact of age on M. tuberculosis host-pathogen interactions following infection of primary alveolar macrophages derived from young and aged rhesus macaques. Of specific interest to us was whether the mycobactericidal capacity of autophagic macrophages was reduced in older animals since decreased autophagosome formation and autophagolysosomal fusion has been observed in other cells types of aged animals. Our data demonstrate that alveolar macrophages from old RM are as competent as those from young animals for autophagic clearance of M. tuberculosis infection and controlling mycobacterial replication. While our data do not reveal significant differences between alveolar macrophage responses to M. tuberculosis by young and old animals, these studies are the first to functionally characterize autophagic clearance of M. tuberculosis by alveolar macrophages from RM.
Power-Normalized Cepstral Coefficients (PNCC) for Robust Speech Recognition

This paper presents a new feature extraction algorithm called power normalized Cepstral coefficients (PNCC) that is motivated by auditory processing. Major new features of PNCC processing include the use of a power-law nonlinearity that replaces the traditional log nonlinearity used in MFCC coefficients, a noise-suppression algorithm based on asymmetric filtering that suppresses background excitation, and a module that accomplishes temporal masking. We also propose the use of medium-time power analysis in which environmental parameters are estimated over a longer duration than is commonly used for speech, as well as frequency smoothing. Experimental results demonstrate that PNCC processing provides substantial improvements in recognition accuracy compared to MFCC and PLP processing for speech in the presence of various types of additive noise and in reverberant environments, with only slightly greater computational cost than conventional MFCC processing, and without degrading the recognition accuracy that is observed while training and testing using clean speech. PNCC processing also provides better recognition accuracy in noisy environments than techniques such as vector Taylor series (VTS) and the ETSI advanced front end (AFE) while requiring much less computation. We describe an implementation of PNCC using “online processing” that does not require future knowledge of the input.
Molecular Characterisation of Trimethoprim Resistance in Escherichia coli and Klebsiella pneumoniae during a Two Year Intervention on Trimethoprim Use

Background Trimethoprim resistance is increasing in Enterobacteriaceae. In 2004-2006 an intervention on trimethoprim use was conducted in Kronoberg County, Sweden, resulting in 85% reduction in trimethoprim prescriptions. We investigated the distribution of dihydrofolate reductase (dfr)-genes and integrons in Escherichia coli and Klebsiella pneumoniae and the effect of the intervention on this distribution. Methodology/Principal Findings Consecutively isolated E. coli (n = 320) and K. pneumoniae (n = 54) isolates phenotypicaly resistant to trimethoprim were studied. All were investigated for the presence of dfrA1, dfrA5, dfrA7, dfrA8, dfrA12, dfrA14, dfrA17 and integrons class I and II. Isolates negative for the seven dfr-genes (n = 12) were also screened for dfr2d, dfrA3, dfrA9, dfrA10, dfrA24 and dfrA26. These genes accounted for 96% of trimethoprim resistance in E. coli and 69% in K. pneumoniae. The most prevalent was dfrA1 in both species. This was followed by dfrA17 in E. coli which was only found in one K. pneumoniae isolate. Class I and II Integrons were more common in E. coli (85%) than in K. pneumoniae (57%). The distribution of dfr-genes did not change during the course of the 2-year intervention. Conclusions/Significance The differences observed between the studied species in terms of dfr-gene and integron prevalence indicated a low rate of dfr-gene transfer between these two species and highlighted the possible role of narrow host range plasmids in the spread of trimethoprim resistance. The stability of dfr-genes, despite large changes in the selective pressure, indirectly suggests a low fitness cost of dfr-gene carriage.
Correlation of Maximum Aortic and Carotid Flow Acceleration in Chronically Instrumented Dogs

Peak flow acceleration measured in the common carotid artery was compared with peak flow acceleration measured in the ascending aorta of five chronically instrumented dogs. Electromagnetic flow sensors, myocardial electrocardiographic leads, right atrial catheters, and coronary occluders were implanted through an incision of the chest at the fourth intercostal space and a ventral midline incision of the neck under sterile conditions while the dogs were anesthetized with sodium pentobarbital. Experiments began 10 days after surgery. We investigated the response to exercise, to 60-second occlusions of the circumflex branch, the anterior descending branch, or both branches of the left coronary artery, to induction of short-acting barbiturate anesthesia, and to intravenous infusion of three concentrations each of isoproterenol (0.8, 1.5–3.0, and 4.0 μg/min), l-norepinephrine (0.8, 2.0, and 4.0 μg/min), and acetylcholine (0.3–0.5, 0.8–2.0, and 4.0 mg/ min). During coronary occlusion, exercise, and induction of anesthesia, both accelerations changed in the same direction and approximately to the same extent. During isoproterenol infusion, both accelerations increased, but the maximum carotid flow acceleration increased more than did the maximum aortic flow acceleration. When l-norepinephrine was infused, the changes were small and were not always in the same direction. When acetylcholine was infused, peak carotid flow acceleration decreased. Peak carotid flow acceleration might be useful as an indirect measure of myocardial mechanical performance during coronary occlusion, anesthesia, and exercise, except during potent peripheral vasodilation like that caused by acetylcholine.
Effects of Ionizing Radiation on Embryos of the Tardigrade Milnesium cf. tardigradum at Different Stages of Development

Tardigrades represent one of the most desiccation and radiation tolerant animals on Earth, and several studies have documented their tolerance in the adult stage. Studies on tolerance during embryological stages are rare, but differential effects of desiccation and freezing on different developmental stages have been reported, as well as dose-dependent effect of gamma irradiation on tardigrade embryos. Here, we report a study evaluating the tolerance of eggs from the eutardigrade Milnesium cf. tardigradum to three doses of gamma radiation (50, 200 and 500 Gy) at the early, middle, and late stage of development. We found that embryos of the middle and late developmental stages were tolerant to all doses, while eggs in the early developmental stage were tolerant only to a dose of 50 Gy, and showed a declining survival with higher dose. We also observed a delay in development of irradiated eggs, suggesting that periods of DNA repair might have taken place after irradiation induced damage. The delay was independent of dose for eggs irradiated in the middle and late stage, possibly indicating a fixed developmental schedule for repair after induced damage. These results show that the tolerance to radiation in tardigrade eggs changes in the course of their development. The mechanisms behind this pattern are unknown, but may relate to changes in mitotic activities over the embryogenesis and/or to activation of response mechanisms to damaged DNA in the course of development.
VLSI placement and area optimization using a genetic algorithm to breed normalized postfix expressions

We present a genetic algorithm (GA) that uses a slicing tree construction process for the placement and area optimization of soft modules in very large scale integration floorplan design. We have overcome the serious representational problems usually associated with encoding slicing floorplans into GAs and have obtained excellent (often optimal) results for module sets with up to 100 rectangles. The slicing tree construction process used by our GA to generate the floorplans has a runtime scaling of O(n lg n). This compares very favorably with other recent approaches based on nonslicing floorplans that require much longer runtimes. We demonstrate that our GA outperforms a simulated annealing implementation with the same representation and mutation operators as the GA.