Miracle-dz/UniFAR-FTUs huggingface dataset:
3D Pseudocontinuous Arterial Spin-Labeling MR Imaging in the Preoperative Evaluation of Gliomas

Fifty-eight patients with pathologically confirmed gliomas underwent preoperative 3D pseudocontinuous arterial spin-labeling and ROC curves were generated for parameters to distinguish high-grade from low-grade gliomas. Both maximum CBF and maximum relative CBF were significantly higher in high-grade than in low-grade gliomas. After adjustment for age, a higher maximum CBF and higher maximum relative CBF were associated with worse progression-free survival. BACKGROUND AND PURPOSE: Previous studies showed conflicting results concerning the value of CBF maps obtained from arterial spin-labeling MR imaging in grading gliomas. This study was performed to investigate the effectiveness of CBF maps derived from 3D pseudocontinuous arterial spin-labeling in preoperatively assessing the grade, cellular proliferation, and prognosis of gliomas. MATERIALS AND METHODS: Fifty-eight patients with pathologically confirmed gliomas underwent preoperative 3D pseudocontinuous arterial spin-labeling. The receiver operating characteristic curves for parameters to distinguish high-grade gliomas from low-grade gliomas were generated. Pearson correlation analysis was used to assess the correlation among parameters. Survival analysis was conducted with Cox regression. RESULTS: Both maximum CBF and maximum relative CBF were significantly higher in high-grade gliomas than in low-grade gliomas (P < .001). The areas under the curve for maximum CBF and maximum relative CBF in distinguishing high-grade gliomas from low-grade gliomas were 0.828 and 0.863, respectively. Both maximum CBF and maximum relative CBF had no correlation with the Ki-67 index in all subjects and had a moderate negative correlation with the Ki-67 index in glioblastomas (r = −0.475, −0.534, respectively). After adjustment for age, a higher maximum CBF (P = .008) and higher maximum relative CBF (P = .005) were associated with worse progression-free survival in gliomas, while a higher maximum relative CBF (P = .033) was associated with better overall survival in glioblastomas. CONCLUSIONS: 3D pseudocontinuous arterial spin-labeling–derived CBF maps are effective in preoperative evaluation of gliomas. Although gliomas with a higher blood flow are more malignant, glioblastomas with a lower blood flow are likely to be more aggressive.
Modeling control of a snake robot with switching constraints

This paper describes modeling and control of a snake robot which can switch grounded parts dynamically. A snake lifts up some parts of its body and dynamically switches grounded parts during locomotion, for example, sinus-lifting and sidewinding motion. We model the lifting up 3D motion of the snake as a switching constraints system in 2D motion and propose the control strategy for the trajectory tracking with switching conditions for the static stability. Simulations show that the decrease of the input norm is accomplished by switching constraints.
Changes in Listing Plane Thickness Caused by Vestibular Schwannoma: A Parameter for Evaluating the Accuracy of the Gravity-Oriented Internal Model

Objective Three-dimensional analysis of video-oculograms can be used to calculate Listing plane for patients and experimental subjects. Listing plane reflects the head’s orientation with respect to gravity, which suggests that the plane is derived from otolithic vestibular input, itself, or from a gravity-oriented internal model constructed through integration of visual, vestibular, and proprioceptive sensory inputs. The goal of this study was to determine whether the Listing plane can serve as a parameter for evaluating static (peripheral or central) vestibular function. Study Design Prospective study. Setting Tertiary referral center. Patients Healthy subjects and patients with unilateral vestibular schwannoma without any previous treatment. Intervention Diagnostic. Main Outcome Measures Video-oculograms were recorded from healthy subjects (aged 36.8 ± 6.3 yr) and from patients (aged 60.3 ± 7.5 yr) during voluntary gaze with the head in an upright or each-side-down orientation, and the thicknesses of the calculated Listing planes were then compared. Results Results revealed thickening of the Listing plane in patients only when the head was in an impaired-side-down orientation (1.250 ± 0.795 and 1.074 ± 0.759 degrees in the right- and left-side-down head orientations in healthy subjects versus 2.222 ± 1.237 degrees in the impaired-side-down orientation in patients), and this thickening correlated with caloric weakness. By contrast, neither the sensation of postural instability nor postural disturbance in force platform recordings contributed to the thickness of Listing plane. Conclusion The thickness of the Listing plane could be a novel parameter for quantitatively evaluating static vestibular (otolithic) function, although central compensation might exist.
On Reliable Control System Designs

A research effort is summarized which addresses some of the current problems in interfacing systems theory and reliability. Reliability is roughly the probability that a system will perform according to specifications for a given amount of time. The reliability of a system depends on the structure of its components. Systems theory and control theory deal with the response characteristics of a system, which depend on the system dynamics. The concepts necessary to unify the structural and the dynamic properties of a system are defined. The result is a definition of what constitutes a reliable system, from the viewpoint of systems theory, and a methodology which can be used to determine if a given design allows a reliable control system design.
On the Development and Distribution of R Packages: An Empirical Analysis of the R Ecosystem

This paper explores the ecosystem of software packages for R, one of the most popular environments for statistical computing today. We empirically study how R packages are developed and distributed on different repositories: CRAN, BioConductor, R-Forge and GitHub. We also explore the role and size of each repository, the inter-repository dependencies, and how these repositories grow over time. With this analysis, we provide a deeper insight into the extent and the evolution of the R package ecosystem.
A workload-aware mapping approach for data-parallel programs

Much compiler-orientated work in the area of mapping parallel programs to parallel architectures has ignored the issue of external workload. Given that the majority of platforms will not be dedicated to just one task at a time, the impact of other jobs needs to be addressed. As mapping is highly dependent on the underlying machine, a technique that is easily portable across platforms is also desirable. In this paper we develop an approach for predicting the optimal number of threads for a given data-parallel application in the presence of external workload. We achieve 93.7% of the maximum speedup available which gives an average speedup of 1.66 on 4 cores, a factor 1.24 times better than the OpenMP compiler's default policy. We also develop an alternative cooperative model that minimizes the impact on external workload while still giving an improved average speedup. Finally, we evaluate our approach on a separate 8-core machine giving an average 1.33 times speedup over the default policy showing the portability of our approach.
Fast cost-volume filtering for visual correspondence and beyond

Many computer vision tasks can be formulated as labeling problems. The desired solution is often a spatially smooth labeling where label transitions are aligned with color edges of the input image. We show that such solutions can be efficiently achieved by smoothing the label costs with a very fast edge preserving filter. In this paper we propose a generic and simple framework comprising three steps: (i) constructing a cost volume (ii) fast cost volume filtering and (iii) winner-take-all label selection. Our main contribution is to show that with such a simple framework state-of-the-art results can be achieved for several computer vision applications. In particular, we achieve (i) disparity maps in real-time, whose quality exceeds those of all other fast (local) approaches on the Middlebury stereo benchmark, and (ii) optical flow fields with very fine structures as well as large displacements. To demonstrate robustness, the few parameters of our framework are set to nearly identical values for both applications. Also, competitive results for interactive image segmentation are presented. With this work, we hope to inspire other researchers to leverage this framework to other application areas.
Customer classification method for multiple pedestrians using pressure sensors

This paper aims to customer classification age groups by walking data using pressure sensor array. Techniques of the age groups estimation in many retail businesses (for example, convenience stores, supermarkets, shopping malls, etc.) are marketable. Because those techniques are applicable for market research and customer analysis. There are many researches of the age estimation using face images, walking silhouette data, etc. However, there are some problems too. One of problem is that the estimation classes are a few. Moreover, many age estimation systems use some video cameras. Therefore, these systems may invade surveyed person's privacy by taking one's face images. Obviously the pressure sensor does not record one's face images. In this study, this fact is one of merit in using the pressure sensors. The pressure sensor array gets feature quantity including center of gravity, pressure value, area of foot, etc. In this study, our system classifies surveyed persons to 6 age groups as each decade. Here, surveyed persons are 20s-70s. Average estimation accuracy of all age groups is 82.67%. The highest estimation accuracy is 89.33% at 20s and 60s.
Persuasive Cued Click-Points: Design, Implementation, and Evaluation of a Knowledge-Based Authentication Mechanism

This paper presents an integrated evaluation of the Persuasive Cued Click-Points graphical password scheme, including usability and security evaluations, and implementation considerations. An important usability goal for knowledge-based authentication systems is to support users in selecting passwords of higher security, in the sense of being from an expanded effective security space. We use persuasion to influence user choice in click-based graphical passwords, encouraging users to select more random, and hence more difficult to guess, click-points.
Evaluating the Capability of Compilers and Tools to Detect Serial and Parallel Run-time Errors

The ability of system software to detect and issue error messages that help programmers quickly fix serial and parallel run-time errors is an important productivity criterion for developing and maintaining application programs. Over ten thousand run-time error tests and a run-time error detection (RTED) evaluation tool have been developed for the automatic evaluation of run-time error detection capabilities for serial errors and for parallel errors in MPI, OpenMP and UPC programs. Each error message issued by the run-time system is assigned a score from 0 to 5 based on the usefulness of the information to help fix the error quickly. Average scores over error categories are automatically calculated and reported. All tests and the RTED evaluation tool are freely available at the RTED web site http://rted.public. iastate.edu. Many compilers, tools and run-time systems have been evaluated with results posted on this same web site.
Locomotor evolution in the Carnivora ( Mammalia ) : evidence from the elbow joint Thesis for the degree of Filosofie Licentiat

The use of humerus distal trochlea circumference as a body mass predictor for carnivores is explored. Trochlea circumference is found to be highly correlated with body mass in carnivores, (r2=0.952, SEE=0.136, p<0001, n=92). Scaling appears to be uniform throughout the order Carnivora, regardless of foot posture. Some degree of differential scaling between carnivore families and between animals of large and small size cannot be ruled out, but this result is inconclusive. A predictive model that allows mass predictions for a broad range of carnivores with a minimum of assumptions is presented. Detransformation bias is corrected by a Maximum Likelihood Estimate. Body mass for eight extinct carnivore species are calculated and these generally conform to earlier mass predictions.
S-nitrosoglutathione (GSNO) is cytotoxic to intracellular amastigotes and promotes healing of topically treated Leishmania major or Leishmania braziliensis skin lesions.

OBJECTIVES This study was designed to verify the cytotoxic activity of S-nitrosoglutathione (GSNO) against intracellular Leishmania amastigotes and to test its efficacy as a topical treatment of localized cutaneous leishmaniasis (LCL) in Leishmania major- or Leishmania braziliensis-infected mice. METHODS Cytotoxic activity of GSNO was verified in L. major-infected THP-1 macrophages. S-nitrosated proteins were detected by immunofluorescence. Topical treatment was done by daily application of a solution of GSNO in PBS to the skin ulcer of Leishmania-infected mice. BALB/c and interferon-γ-knockout (IFN-γ-KO) C57BL/6 mice were infected with L. major and L. braziliensis, respectively. Ulcer size was measured weekly and the parasite loads were determined in the lesion and lymph nodes. Controls received PBS topically or amphotericin B (AMB) intravenously. RESULTS The number of intracellular L. major amastigotes was markedly reduced in GSNO-treated cultures; in these, staining for S-nitrosated proteins was present in the cytoplasm and colocalized with intracellular amastigotes. Topical treatment with GSNO of L. major ulcers in BALB/c mice suppressed lesion growth, reduced the parasite load and induced healing comparable to the effect of intravenously administered AMB. Topical GSNO treatment was also efficient at suppressing lesion growth in IFN-γ-KO mice infected with L. braziliensis. CONCLUSIONS GSNO is cytotoxic to intracellular L. major amastigotes in vitro and had a healing effect on LCL caused by L. major and L. braziliensis in mice. These positive results on the topical therapeutic effect of GSNO in mouse leishmaniasis infections provide the experimental basis for a possible future trial in the treatment of human LCL.
Evaporation-Driven Fast Crystallization of 3D Micro- and Nano-particle Assemblies via Micro Mechanical Systems

Fast crystallization of solid-phase materials in liquid medium is a crucial pre-requisite to achieve the aims of a number of applications for micro-and nano-manufacturing, bio-chemical sensing technology and fundamental colloidal science. Corresponding mechanical systems for those applications are required to accommodate and take advantage of the virtue of multi-phase (liquid, gas, and solid phases) flow phenomenon to accomplish crystallization part for complete functioning. In this dissertation, evaporation-driven fast crystallization of micro-and nano-particles is demonstrated via micro mechanical systems in order to inspire potential implementation of those systems to existing mechanical systems. Various fast crystallizing behaviors of micro, nanoparticles are demonstrated by multi-phase flow in the micro-mechanical systems. Evaporative flows such as open-channel flow, thin liquid-flim flow, and fast, micro-scale evaporative liquid flow on hydrophobic surface are driving fast crystallization of the particles in micro-mechanical systems with sub-5 minute scale. Critical parameters for the analysis of colloidal motions in evaporative flows are identified by conventional thermo-coupled fluid mechanics and numerical values of those parameters were accurately calculated by particle-dynamic incorporated-computations to provide accounts for particle effects in evaporative self-assembly. Finally, electrical and optical characterizations of crystallized 3D lattices are performed to demonstrate the feasibility of the developed systems for rapid, direct characterization of various target species. Experimental, analytical and computational parts of the dissertation complement each other with active cross-talks and reinforce the thesis argument that evaporation-driven multi-phase flow can be applied for the improvement of micro-and nano-manufacturing technologies, bio-chemical assay technologies and the development of platforms for fundamental colloidal sciences.
The Role of Regulatory B Cell-Like Malignant Cells and Treg Cells in the Mouse Model of BCL1 Tumor Dormancy

Cancer dormancy is a clinical state in which residual tumor cells persist for long periods of time but do not cause detectable disease. In the mouse B cell lymphoma model (BCL1), dormancy can be induced and maintained by immunizing mice with a soluble form of the IgM expressed on the surface of the tumor cells. Immunization induces an anti-idiotype antibody response that maintains dormancy. Mice with dormant tumor have low numbers of BCL1 cells in their spleens that divide and are killed at the same rate. When the anti-Id antibodies wane, the tumor cells grow rapidly and kill the host. Spleens from tumor-bearing mice contain both effector (CD4+ and CD8+) and regulatory T cells (Tregs). In other tumor models, it has been reported that Tregs promote tumor progression by preventing effector cells from killing the tumor. In this report, we demonstrate that the tumor site with rapidly dividing BCL1 cells has fewer Tregs than the tumor site harboring dormant BCL1 cells. In both cases, the Tregs were equally suppressive in vitro. In spleens from mice with actively growing tumor, CD8+ but not CD4+ T cells were virtually absent. In vitro analysis demonstrated a tumor-mediated elimination of CD8+ T cells that was contact dependent and involved the caspase-3 pathway. Most importantly, we found that the BCL1 cells expressed characteristics of B10 regulatory B cells, i.e., they were CD1dhiCD5+ and secreted high levels of IL-10. These BCL1 tumor cells can inhibit anti-tumor immune responses by depleting CD8+ effector T cells.
Various shapes of silicon freestanding microfluidic channels and microstructures in one-step lithography

In this research, we have developed and demonstrated a fabrication method for the formation of various shapes of silicon freestanding microfluidic channels and microstructures in one-step photolithography. The fabrication process utilizes the silicon direct wafer bonding with silicon nitride as an intermediate layer, local oxidation of the silicon (LOCOS) process and wet anisotropic etching. Two different types of etchants (non-ionic surfactant (Triton-X-100) added and pure 25 wt% TMAH solutions) are used in series to perform silicon anisotropic etching. Surfactant-added tetramethyl ammonium hydroxide (TMAH) is employed to define the shapes of the structures, while pure TMAH is used to get high undercutting for their fast releasing. The non-ionic surfactant is preferred considering the complementary metal-oxide semiconductor (CMOS) post process issue of wet anisotropic etching. The undercutting at sharp and rounded concave corners, edges aligned along ⟨1 0 0⟩ directions, is measured and analyzed in both pure and surfactant-added TMAH solutions. Mask design issues that must be taken into consideration for the fabrication of desired shape and size structures are also presented.
Probabilistic Decision Graphs - Combining Verification And Ai Techniques For Probabilistic Inference

We adopt probabilistic decision graphs developed in the field of automated verification as a tool for probabilistic model representation and inference. We show that probabilistic inference has linear time complexity in the size of the probabilistic decision graph, that the smallest probabilistic decision graph for a given distribution is at most as large as the smallest junction tree for the same distribution, and that in some cases it can in fact be much smaller. Behind these very promising features of probabilistic decision graphs lies the fact that they integrate into a single coherent framework a number of representational and algorithmic optimizations developed for Bayesian networks (use of hidden variables, context-specific independence, structured representation of conditional probability tables).
Variational Integrators and the Newmark Algorithm for Conservative and Dissipative Mechanical Systems

The purpose of this work is twofold. First, we demonstrate analytically that the classical Newmark family as well as related integration algorithms are variational in the sense of the Veselov formulation of discrete mechanics. Such variational algorithms are well known to be symplectic and momentum preserving and to often have excellent global energy behavior. This analytical result is veried through numerical examples and is believed to be one of the primary reasons that this class of algorithms performs so well. Second, we develop algorithms for mechanical systems with forcing, and in particular, for dissipative systems. In this case, we develop integrators that are based on a discretization of the Lagrange d'Alembert principle as well as on a variational formulation of dissipation. It is demonstrated that these types of structured integrators have good numerical behavior in terms of obtaining the correct amounts by which the energy changes over the integration run.
Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligase

Single-stranded DNA molecules (ssDNA) annealed to an RNA splint are notoriously poor substrates for DNA ligases. Herein we report the unexpectedly efficient ligation of RNA-splinted DNA by Chlorella virus DNA ligase (PBCV-1 DNA ligase). PBCV-1 DNA ligase ligated ssDNA splinted by RNA with kcat ≈ 8 x 10−3 s−1 and KM < 1 nM at 25°C under conditions where T4 DNA ligase produced only 5′-adenylylated DNA with a 20-fold lower kcat and a KM ≈ 300 nM. The rate of ligation increased with addition of Mn2+, but was strongly inhibited by concentrations of NaCl >100 mM. Abortive adenylylation was suppressed at low ATP concentrations (<100 µM) and pH >8, leading to increased product yields. The ligation reaction was rapid for a broad range of substrate sequences, but was relatively slower for substrates with a 5′-phosphorylated dC or dG residue on the 3′ side of the ligation junction. Nevertheless, PBCV-1 DNA ligase ligated all sequences tested with 10-fold less enzyme and 15-fold shorter incubation times than required when using T4 DNA ligase. Furthermore, this ligase was used in a ligation-based detection assay system to show increased sensitivity over T4 DNA ligase in the specific detection of a target mRNA.
Parallel hierarchical sampling: a practical multiple-chains sampler for Bayesian model selection

This paper introduces the parallel hierarchical sampler (PHS), a Markov chain Monte Carlo algorithm using several chains simultaneously. The connections between PHS and the parallel tempering (PT) algorithm are illustrated, convergence of PHS joint transition kernel is proved and and its practical advantages are emphasized. We illustrate the inferences obtained using PHS, parallel tempering and the Metropolis-Hastings algorithm for three Bayesian model selection problems, namely Gaussian clustering, the selection of covariates for a linear regression model and the selection of the structure of a treed survival model.