Miracle-dz/UniFAR-FTUs huggingface dataset:
OctoPOS : A Parallel Operating System for Invasive Computing

Invasive Computing is a research program that aims at developing a new paradigm to address the hardwareand software challenges of managing and using massively-parallel MPSoCs of the years 2020 and beyond. The program encompasses twelve projects from the areas of computer architecture, system software, programming systems, algorithm engineering and applications. The core idea is to let applications manage the available computing resources on a local scope and to provide means for a dynamic and fine-grained expansion and contraction of parallelism. In this paper we present initial thoughts on operating-system support for the invasive paradigm and discuss first experimental results with run-time support for invasive programs.
Knocking-Down Cyclin A2 by siRNA Suppresses Apoptosis and Switches Differentiation Pathways in K562 Cells upon Administration with Doxorubicin

Cyclin A2 is critical for the initiation of DNA replication, transcription and cell cycle regulation. Cumulative evidences indicate that the deregulation of cyclin A2 is tightly linked to the chromosomal instability, neoplastic transformation and tumor proliferation. Here we report that treatment of chronic myelogenous leukaemia K562 cells with doxorubicin results in an accumulation of cyclin A2 and follows by induction of apoptotic cell death. To investigate the potential preclinical relevance, K562 cells were transiently transfected with the siRNA targeting cyclin A2 by functionalized single wall carbon nanotubes. Knocking down the expression of cyclin A2 in K562 cells suppressed doxorubicin-induced growth arrest and cell apoptosis. Upon administration with doxorubicin, K562 cells with reduced cyclin A2 showed a significant decrease in erythroid differentiation, and a small fraction of cells were differentiated along megakaryocytic and monocyte-macrophage pathways. The results demonstrate the pro-apoptotic role of cyclin A2 and suggest that cyclin A2 is a key regulator of cell differentiation. To the best of our knowledge, this is the first report that knocking down expression of one gene switches differentiation pathways of human myeloid leukemia K562 cells.
E-timed Workflow Nets

In this paper, e-timed workflow nets are introduced, and a characterization of the soundness property for them is provided. This characterization is based on boundedness and liveness as for classical workflow nets. It is shown that the properties of boundedness and liveness for e-timed Petri nets can be reduced to the same properties for Petri nets with zero-tests on bounded places. As these two properties are decidable for Petri nets with zero-tests on bounded places, the soundness property for e-timed workflow nets is decidable
Rifampicin for Continuation Phase Tuberculosis Treatment in Uganda: A Cost-Effectiveness Analysis

Background In Uganda, isoniazid plus ethambutol is used for 6 months (6HE) during the continuation treatment phase of new tuberculosis (TB) cases. However, the World Health Organization (WHO) recommends using isoniazid plus rifampicin for 4 months (4HR) instead of 6HE. We compared the impact of a continuation phase using 6HE or 4HR on total cost and expected mortality from the perspective of the Ugandan national health system. Methodology/Principal Findings Treatment costs and outcomes were determined by decision analysis. Median daily drug price was US$0.115 for HR and US$0.069 for HE. TB treatment failure or relapse and mortality rates associated with 6HE vs. 4HR were obtained from randomized trials and systematic reviews for HIV-negative (46% of TB cases; failure/relapse –6HE: 10.4% vs. 4HR: 5.2%; mortality –6HE: 5.6% vs. 4HR: 3.5%) and HIV-positive patients (54% of TB cases; failure or relapse –6HE: 13.7% vs. 4HR: 12.4%; mortality –6HE: 16.6% vs. 4HR: 10.5%). When the initial treatment is not successful, retreatment involves an additional 8-month drug-regimen at a cost of $110.70. The model predicted a mortality rate of 13.3% for patients treated with 6HE and 8.8% for 4HR; average treatment cost per patient was predicted at $26.07 for 6HE and $23.64 for 4HR. These results were robust to the inclusion of MDR-TB as an additional outcome after treatment failure or relapse. Conclusions/Significance Combination therapy with 4HR in the continuation phase dominates 6HE as it is associated with both lower expected costs and lower expected mortality. These data support the WHO recommendation to transition to a continuation phase comprising 4HR.
Factors affecting the appearance of the hump charge movement component in frog cut twitch fibers

Charge movement was measured in frog cut twitch fibers with the double Vaseline gap technique. Five manipulations listed below were applied to investigate their effects on the hump component (I gamma) in the ON segments of TEST minus CONTROL current traces. When external Cl-1 was replaced by MeSO3- to eliminate Cl current, I gamma peaked earlier due to a few millivolts shift of the voltage dependence of I gamma kinetics in the negative direction. The Q-V plots in the TEA.Cl and TEA.MeSO3 solutions were well fitted by a sum of two Boltzmann distribution functions. The more steeply voltage-dependent component (Q gamma) had a V approximately 6 mV more negative in the TEA.MeSO3 solution than in the TEA.Cl solution. These voltage shifts were partially reversible. When creatine phosphate in the end pool solution was removed, the I gamma hump disappeared slowly over the course of 20-30 min, partly due to a suppression of Q gamma. The hump reappeared when creatine phosphate was restored. When 0.2-1.0 mM Cd2+ was added to the center pool solution to block inward Ca current, the I gamma hump became less prominent due to a prolongation in the time course of I gamma but not to a suppression of Q gamma. When the holding potential was changed from -90 to -120 mV, the amplitude of I beta was increased, thereby obscuring the I gamma hump. Finally, when a cut fiber was stimulated repetitively, I gamma lost its hump appearance because its time course was prolonged. In an extreme case, a 5-min resting interval was insufficient for a complete recovery of the waveform. In general, a stimulation rate of once per minute had a negligible effect on the shape of I gamma. Of the five manipulations, MeSO3- has the least perturbation on the appearance of I gamma and is potentially a better substitute for Cl- than SO2-(4) in eliminating Cl current if the appearance of the I gamma hump is to be preserved.
Comparison of foam swabs and toothbrushes as oral hygiene interventions in mechanically ventilated patients: a randomised split mouth study

Introduction During critical illness, dental plaque may serve as a reservoir of respiratory pathogens. This study compared the effectiveness of toothbrushing with a small-headed toothbrush or a foam-headed swab in mechanically ventilated patients. Methods This was a randomised, assessor-blinded, split-mouth trial, performed at a single critical care unit. Adult, orally intubated patients with >20 teeth, where >24 hours of mechanical ventilation was expected were included. Teeth were cleaned 12-hourly using a foam swab or toothbrush (each randomly assigned to one side of the mouth). Cleaning efficacy was based on plaque scores, gingival index and microbial plaque counts. Results High initial plaque (mean=2.1 (SD 0.45)) and gingival (mean=2.0 (SD 0.54)) scores were recorded for 21 patients. A significant reduction compared with initial plaque index occurred using both toothbrushes (mean change=−1.26, 95% CI −1.57 to −0.95; p<0.001) and foam swabs (mean change=−1.28, 95% CI −1.54 to −1.01; p<0.001). There was significant reduction in gingival index over time using toothbrushes (mean change=−0.92; 95% CI −1.19 to −0.64; p<0.001) and foam swabs (mean change=−0.85; 95% CI −1.10 to −0.61; p<0.001). Differences between cleaning methods were not statistically significant (p=0.12 for change in gingival index; p=0.24 for change in plaque index). There was no significant change in bacterial dental plaque counts between toothbrushing (mean change 3.7×104 colony-forming units (CFUs); minimum to maximum (−2.5×1010 CFUs, 8.7×107 CFUs)) and foam swabs (mean change 9×104 CFUs; minimum to maximum (−3.1×1010 CFUs, 3.0×107 CFUs)). Conclusions Patients admitted to adult intensive care had poor oral health, which improved after brushing with a toothbrush or foam swab. Both interventions were equally effective at removing plaque and reducing gingival inflammation. Trial registration number NCT01154257; Pre-results.
Objective Lotteries as Ambiguous Objects : Allais , Ellsberg , and Hedging ∗

We derive axiomatically a model in which the Decision Maker can exhibit simultaneously both the Allais and the Ellsberg paradoxes in the standard setup of Anscombe and Aumann (1963). Using the notion of ‘subjective’, or ‘outcome’ mixture of Ghirardato et al. (2003), we define a novel form of hedging for objective lotteries, and introduce a novel axiom which is a generalized form of preferences for hedging. We show that this axiom, together with other standard ones, is equivalent to a representation in which the agent reacts to ambiguity using multiple priors like the MaxMin Expected Utility model of Gilboa and Schmeidler (1989), generating an Ellsberg-like behavior, while at the same time, she treats also objective lotteries as ‘ambiguous objects,’ and use a fixed (and unique) set of priors to evaluate them – generating an Allais-like behavior. We show that this representation is equivalent to one in which the agent evaluates lotteries using a set of concave rank-dependent utility functionals. A comparative notion of preference for hedging is also introduced. JEL: D81
Relative kinematics of the rib cage and abdomen during speech and nonspeech behaviors of 15-month-old children.

Speech motor control emerges in the neurophysiologic context of widely distributed, powerful coordinative mechanisms, including those mediating respiratory function. It is unknown, however, whether developing children are able to exploit the capabilities of neural circuits controlling homeostasis for the production of speech and voice. Speech and rest breathing were investigated in eleven 15-month-old children using inductance plethysmography (Respitrace). Rib cage and abdominal kinematics were studied using a time-varying correlational index of thoracoabdominal coupling (i.e., reflecting the synchrony of movement of the rib cage and abdomen) as well as simple classification of the moment-to-moment kinematic relationship of these two functional components (i.e., concurrent expansion or compression, or oppositional movement). Results revealed markedly different patterns of movement for rest breathing and speech breathing, although within types of vocalization (nonspeech vocalization, babbling, true word production) no differences were apparent. Whereas rest breathing was characterized by tight coupling of rib cage and abdominal movement (average correlation coefficients usually exceeded .90), speech breathing exhibited weak coupling (the correlation coefficient ranged widely, but averaged about .60). Furthermore, speech production by these toddlers included the occurrence of both rib cage and abdominal paradoxing, which are observed infrequently in adult speakers. These results fail to support the suggestion that speech emerges from the extant coordinative organization of rest breathing. Rather, even in its earliest stages breathing for speech and voice exhibits kinematic properties distinct from those of other observed behaviors.
Online Learning of Task-specific Word Representations with a Joint Biconvex Passive-Aggressive Algorithm

This paper presents a new, efficient method for learning task-specific word vectors using a variant of the Passive-Aggressive algorithm. Specifically, this algorithm learns a word embedding matrix in tandem with the classifier parameters in an online fashion, solving a bi-convex constrained optimization at each iteration. We provide a theoretical analysis of this new algorithm in terms of regret bounds, and evaluate it on both synthetic data and NLP classification problems, including text classification and sentiment analysis. In the latter case, we compare various pre-trained word vectors to initialize our word embedding matrix, and show that the matrix learned by our algorithm vastly outperforms the initial matrix, with performance results comparable or above the state-of-the-art on these tasks.
The impact of the CERAD‐NP on diagnosis of cognitive deficiencies in late onset depression and Alzheimer's disease

To identify the most appropriate test combination for distinguishing between late onset depression (LOD) and Alzheimer's disease (AD). To achieve this objective, the Consortium to Establish a Register for Alzheimer's Disease‐Neuropsychological Battery (CERAD‐NP) data of patients diagnosed with these two conditions were analyzed using multiple regression analysis.
GGO Nodule Volume-Preserving Nonrigid Lung Registration Using GLCM Texture Analysis

In lung cancer screening, benign and malignant nodules can be classified through nodule growth assessment by the registration and, then, subtraction between follow-up computed tomography scans. During the registration, the volume of nodule regions in the floating image should be preserved, whereas the volume of other regions in the floating image should be aligned to that in the reference image. However, ground glass opacity (GGO) nodules are very elusive to automatically segment due to their inhomogeneous interior. In other words, it is difficult to automatically define the volume-preserving regions of GGO nodules. In this paper, we propose an accurate and fast nonrigid registration method. It applies the volume-preserving constraint to candidate regions of GGO nodules, which are automatically detected by gray-level cooccurrence matrix (GLCM) texture analysis. Considering that GGO nodules can be characterized by their inner inhomogeneity and high intensity, we identify the candidate regions of GGO nodules based on the homogeneity values calculated by the GLCM and the intensity values. Furthermore, we accelerate our nonrigid registration by using Compute Unified Device Architecture (CUDA). In the nonrigid registration process, the computationally expensive procedures of the floating-image transformation and the cost-function calculation are accelerated by using CUDA. The experimental results demonstrated that our method almost perfectly preserves the volume of GGO nodules in the floating image as well as effectively aligns the lung between the reference and floating images. Regarding the computational performance, our CUDA-based method delivers about 20× faster registration than the conventional method. Our method can be successfully applied to a GGO nodule follow-up study and can be extended to the volume-preserving registration and subtraction of specific diseases in other organs (e.g., liver cancer).
Storage, mixing, and fluxes of water in the critical zone across northern environments inferred by stable isotopes of soil water

Quantifying soil water storage, mixing, and release via recharge, transpiration, and evaporation is essential for a better understanding of critical zone processes. Here, we integrate stable isotope (2H and 18O of soil water, precipitation, and groundwater) and hydrometric (soil moisture) data from 5 long‐term experimental catchments along a hydroclimatic gradient across northern latitudes: Dry Creek (USA), Bruntland Burn (Scotland), Dorset (Canada), Krycklan (Sweden), and Wolf Creek (Canada). Within each catchment, 6 to 11 isotope sampling campaigns occurred at 2 to 4 sampling locations over at least 1 year. Analysis for 2H and 18O in the bulk pore water was done for >2,500 soil samples either by cryogenic extraction (Dry Creek) or by direct equilibration (other sites). The results showed a similar general pattern that soil water isotope variability reflected the seasonality of the precipitation input signal. However, pronounced differences among sampling locations occurred regarding the isotopic fractionation due to evaporation. We found that antecedent precipitation volumes mainly governed the fractionation signal, temperature and evaporation rates were of secondary importance, and soil moisture played only a minor role in the variability of soil water evaporation fractionation across the hydroclimatic gradient. We further observed that soil waters beneath conifer trees were more fractionated than beneath heather shrubs or red oak trees, indicating higher soil evaporation rates in coniferous forests. Sampling locations closer to streams were more damped and depleted in their stable isotopic composition than hillslope sites, revealing increased subsurface mixing towards the saturated zone and a preferential recharge of winter precipitation. Bulk soil waters generally comprised a high share of waters older than 14 days, which indicates that the water in soil pores are usually not fully replaced by recent infiltration events. The presented stable isotope data of soil water were, thus, a useful tool to track the spatial variability of water fluxes within and from the critical zone. Such data provide invaluable information to improve the representation of critical zone processes in spatially distributed hydrological models.
Disrupted Functional Brain Connectivity in Partial Epilepsy: A Resting-State fMRI Study

Examining the spontaneous activity to understand the neural mechanism of brain disorder is a focus in recent resting-state fMRI. In the current study, to investigate the alteration of brain functional connectivity in partial epilepsy in a systematical way, two levels of analyses (functional connectivity analysis within resting state networks (RSNs) and functional network connectivity (FNC) analysis) were carried out on resting-state fMRI data acquired from the 30 participants including 14 healthy controls(HC) and 16 partial epilepsy patients. According to the etiology, all patients are subdivided into temporal lobe epilepsy group (TLE, included 7 patients) and mixed partial epilepsy group (MPE, 9 patients). Using group independent component analysis, eight RSNs were identified, and selected to evaluate functional connectivity and FNC between groups. Compared with the controls, decreased functional connectivity within all RSNs was found in both TLE and MPE. However, dissociating patterns were observed within the 8 RSNs between two patient groups, i.e, compared with TLE, we found decreased functional connectivity in 5 RSNs increased functional connectivity in 1 RSN, and no difference in the other 2 RSNs in MPE. Furthermore, the hierarchical disconnections of FNC was found in two patient groups, in which the intra-system connections were preserved for all three subsystems while the lost connections were confined to intersystem connections in patients with partial epilepsy. These findings may suggest that decreased resting state functional connectivity and disconnection of FNC are two remarkable characteristics of partial epilepsy. The selective impairment of FNC implicated that it is unsuitable to understand the partial epilepsy only from global or local perspective. We presumed that studying epilepsy in the multi-perspective based on RSNs may be a valuable means to assess the functional changes corresponding to specific RSN and may contribute to the understanding of the neuro-pathophysiological mechanism of epilepsy.
AGILE SOFTWARE ARCHITECTURE RECOVERY THROUGH EXISTING SOLUTIONS AND DESIGN PATTERNS

Software architectures evolve over time due to requirement and technology changes. Hence, software architecture recovery is often necessary to capture and document existing systems to effectively support product evolution and maintenance. Architectures of existing systems can be recovered using reverse engineering techniques. Reverse engineering deals with deriving higher-level descriptions of a software system from existing software artifacts, primarily source code. Reverse engineering of source code, often, is a time consuming task. For reasons of limited resources or competition, software architectures could be recovered more efficiently by studying solutions from similar systems. This paper presents an approach for rapid and agile software architecture recovery in a mature domain, network applications. We demonstrate a case study for software architecture recovery by examining an existing architecture in the same domain. The existing architecture help derive a conceptual description for the target system. Meanwhile, some well-known design patterns in the similar domain are used to compare with the target system. The knowledge gained from design patterns provides more detailed information. The process is coupled with iterative reviews of the source code to refine the recovered software architecture.
Privacy against statistical inference

We propose a general statistical inference framework to capture the privacy threat incurred by a user that releases data to a passive but curious adversary, given utility constraints. We show that applying this general framework to the setting where the adversary uses the self-information cost function naturally leads to a non-asymptotic information-theoretic approach for characterizing the best achievable privacy subject to utility constraints. Based on these results we introduce two privacy metrics, namely average information leakage and maximum information leakage. We prove that under both metrics the resulting design problem of finding the optimal mapping from the user's data to a privacy-preserving output can be cast as a modified rate-distortion problem which, in turn, can be formulated as a convex program. Finally, we compare our framework with differential privacy.
The sarcomere length-tension relation in skeletal muscle

Tension development during isometric tetani in single fibers of frog semitendinosus muscle occurs in three phases: (a) in initial fast-rise phase; (b) a slow-rise phase; and (c) a plateau, which lasts greater than 10 s. The slow-rise phase has previously been assumed to rise out of a progressive increase of sarcomere length dispersion along the fiber (Gordon et al. 1966. J. Physiol. [Lond.]. 184:143--169;184:170-- 192). Consequently, the "true" tetanic tension has been considered to be the one existing before the onset of the slow-rise phase; this is obtained by extrapolating the slowly rising tension back to the start of the tetanus. In the study by Gordon et al. (1966. J. Physiol. [Lond.] 184:170--192), as well as in the present study, the relation between this extrapolated tension and sarcomere length gave the familiar linear descending limb of the length-tension relation. We tested the assumption that the slow rise of tension was due to a progressive increase in sarcomere length dispersion. During the fast rise, the slow rise, and the plateau of tension, the sarcomere length dispersion at any area along the muscle was less than 4% of the average sarcomere length. Therefore, a progressive increase of sarcomere length dispersion during contraction appears unable to account for the slow rise of tetanic tension. A sarcomere length-tension relation was constructed from the levels of tension and sarcomere length measured during the plateau. Tension was independent of sarcomere length between 1.9 and 2.6 microgram, and declined to 50% maximal at 3.4 microgram. This result is difficult to reconcile with the cross-bridge model of force generation.