Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Circulating Tumor DNA as a Non-Invasive Tool for Monitoring the Progression of Colorectal Cancer

Background Liquid biopsy has been proposed to be a promising noninvasive tool to obtain information on tumor progression. Through a clinical observation of a case series of 6 consecutive patients, we aim to determine the value of circulating tumor DNA (ctDNA) for monitoring the tumor burden during the treatment of colorectal cancer (CRC). Materials and Methods We used capture sequencing of 545 genes to identify somatic alternations in primary tumor tissues of the six CRC patients who underwent radical surgery and in 23 plasma samples collected at serial time points. We compared the mutation patterns and variant allele frequencies (VAFs) between the matched tissue and the plasma samples and evaluated the potential advantage of using ctDNA as a better tumor load indicator to detect disease relapse over carcinoembryonic antigen (CEA), cancer antigen (CA) 19–9 and imaging studies. Results We identified low-frequency mutations with a mean VAF of 0.88% (corresponding to a mean tumor burden of 0.20ng/mL) in the preoperative plasmas of four patients with locally advanced CRC and a subset of mutations shared by their primary tumors. The tumor loads appeared a sudden decrease upon surgery or other adjuvant treatments and then generally maintained at low levels (0.092ng/mL) until disease recurred. ctDNA increased by 13-fold when disease relapsed in one patient while the CEA and CA 19–9 levels remained normal. In this patient, all six somatic mutations identified in the preoperative plasma were detected in the recrudescent plasma again, with five mutations showing allele fraction increase. Conclusions We described a multi-time-point profile of ctDNA of CRC patients during the course of comprehensive treatment and observed a correlation of ctDNA level with the clinically evaluated tumor progression. This demonstrated a new strategy by analyzing the heterogeneous ctDNA to evaluate and monitor the tumor burden in the treatment and follow-up of CRC patients, with potentially better potency than conventional biomarkers.
A comparison between person re-identification approaches

In this paper, we presented a comparison between different approaches of person re-identification in camera network based on the-state-of-the-art. We studied the different descriptors of objects for identifying people and existing classifier at the re-identification step. We seek to develop video surveillance systems online in controlled areas and improve their reliability and their processing time. We concluded that using the spatio-temporal information of any person and its biometrics behavioral extracted from the video stream and analyzed then through an online classification represent a modern approach.
On the physical interpretation of singularities in Lanczos-Newman electrodynamics

We discuss the physical nature of elementary singularities arising in the complexified Maxwell field extended into complex spacetime, i.e., in Lanczos-Newman electrodynamics, which may provide a possible link between elementary particle physics and general relativity theory. We show that the translation of the world-line of a bare (e.g., spinless) electric-monopole singularity into imaginary space is adding a magnetic-dimonopole component to it, so that it can be interpreted as a pseudoscalar pion-proton interaction current, consistent which both charge-independent meson theory and zero-order quantum chromodynamics. On the other hand, the interaction current of an electric-monopole intrinsic-magnetic-dipole singularity characteristic of a Dirac electron is obtained by another operation on the world-line, which however does not seem to have a simple geometric interpretation. Nevertheless, both operations can be given a covariant interpretation, which shows that the corresponding interactions necessarily arise on an equal footing, and therefore provides a connection between elementary particles and singularities in general relativity.
Nonlinear k-subspaces based appearances clustering of objects under varying illumination conditions

Unsupervised clustering of image sets of 3D objects has been an active research field within vision community. It is a challenging task since the appearance variation of the same object under different illumination condition is often larger than the appearance variation of different object under the same illumination condition. Some previous methods perform the appearance clustering using k-subspaces algorithm by assuming that the set of images of a Lambertian object approximately reside in a low dimensional linear subspace. This paper further extends the original ksubspaces clustering algorithm to the nonlinear case. The sum of the squares of distance to corresponding feature points of each nonlinear subspace cluster centers is minimized using Expectation-Maximization like iteration procedure. Those distances can be novelly defined via inner product by kernel trick. Experiments on different datasets show that the proposed kernel-based nonlinear k-subspaces clustering algorithm achieves much higher clustering rate than its linear counterpart.
Dynamic pressures in the pial arterial microcirculation.

SHAPIRO, HARVEY M. , DON D. STROMBERG, DENNIS R. LEE, AND CURT A. WIEDERHIELM. Dynamic pressures in the pial arterial microcirculation. Am. J. Physiol. 22 l(1) : 279-283. 197 1 . -Using a modified Wiederhielm servo-micropipet system with pipet tips of 0.5-l p diam, we measured and recorded dynamic arterial pressures in 42 arteries and arterioles of the pial vascular network on the surface of the parietal cortex of eight pentobarbitalanesthetized cats. Aortic pressure, mean central venous pressure, and end-tidal CO:! were also recorded. In branches of the middle cerebral artery as large as 455 p od, pressure was only 61 y0 of aortic pressure. Additional pressure-head loss from these major vessels across the pial arterial bed down to the penetrating arterioles (approx. 25 p od) was only 10 %. These results are compatible with the “pressure equalization reservoir” concept of the pial arterial network.
DTN routing in a mobility pattern space

Routing in delay tolerant networks (DTNs) benefits considerably if one can take advantage of knowledge concerning node mobility. The main contribution of this paper is the definition of a generic routing scheme for DTNs using a high-dimensional Euclidean space constructed upon nodes' mobility patterns. We call this the MobySpace. One way of representing nodes in this space is to give them coordinates that correspond to their probability of being found in each possible location. We present simulation results indicating that such a scheme can be beneficial in a scenario inspired by studies done on real mobility traces. This work should open the way to further use of the virtual space formalism in DTN routing.
Non-invasive 4D blood flow and pressure quantification in central blood vessels via PC-MRI

Purpose of this work is the demonstration of new methods for non-invasive assessment of detailed haemodynamical parameters in central blood vessels based on advanced postprocessing methods. In particular, we present a new finite-element-based method for computing 4D intravascular blood pressure differences. A verification using CFD methods and tests on real image data show the possible value of the method for clinical diagnosis and therapy planning.
Nanofluidic digital PCR for KRAS mutation detection and quantification in gastrointestinal cancer.

BACKGROUND Concomitant quantification of multiple mutant KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) alleles may provide information in addition to that provided by standard mutation-detection procedures. We assessed the feasibility of a nanofluidic digital PCR array platform to detect and quantify KRAS mutations simultaneously in clinically relevant samples. METHODS We assessed 2 groups of patients (colorectal and pancreatic disease): Group 1 consisted of 27 patients with colorectal carcinomas, 14 patients with adenomas, and 5 control individuals; group 2 consisted of 42 patients with pancreatic carcinoma, 4 with adenocarcinomas of the ampulla, and 6 with chronic pancreatitis). Digital PCR was performed with the Digital Array Chip (Fluidigm). RESULTS Nanofluidic digital PCR detected mutant alleles at 0.05% to 0.1%, depending on the variant analyzed. For the colorectal disease group, conventional PCR detected 9 (64%) of 14 adenomas that were positive for KRAS mutants, whereas digital PCR increased this number to 11 (79%) of 14. Sixteen (59%) of 27 carcinomas showed KRAS mutation with conventional PCR. Two additional cases were detected with digital PCR. In 5 cases (3 adenomas, 2 carcinomas), the total number of mutant alleles changed. For the pancreatic disease group, digital PCR increased the number of positive cases from 26 to 34 (81%) and identified ≥ 2 mutant alleles in 25 cases, compared with conventional PCR, which identified multiple KRAS mutant alleles in only 12 cases. A good correlation was observed between results obtained with tumor biopsies and those obtained with pancreatic juice. CONCLUSIONS Digital PCR provides a robust, quantitative measure of the proportion of KRAS mutant alleles in routinely obtained samples. It also allows a better classification of tumors, with potential clinical relevance.
On the possible interactions of varied EFL activities and learning styles with EFL students’ motivational changes

ABSTRACT L2 classroom is a place and process that undergoes an array of incessant and concurrent changes affecting its main agents, i.e. the teacher and students in a non-linear and unpredictable manner. Various aspects of their cognitive and affective potential fluctuate and intensify or weaken depending on what is going on in a particular L2 learning/teaching environment at a particular point of time. The present paper, drawing on the idea of complexity, multifariousness and spatiotemporal situatedness of a language classroom, is intended to examine the likelihood and dynamics of the reciprocal co-occurrence of a range of practical English learning activities, learning styles and changes in motivation. In the first, theoretical part the authors will present literature review with a special regard to the complex dynamic systems perspective on motivation. The second part is devoted to a discussion of findings from the qualitatively and quantitatively oriented research conducted on two groups of English philology students. Data gathering instruments included the questionnaires investigating the subjects’ while-class and after-class involvement, the learning style survey, the teacher's evaluation of conducted classes and participant observation. Obtained results revealed certain patterns of motivational variability in relation to the students’ general learning preferences.
Police power and fettered freedom: regulating coastal freedom camping in New Zealand

Abstract Freedom camping is a form of tourism entailing overnight stays in public open spaces, rather than formal campgrounds. It presents varied challenges for local governments charged with maintaining safe and orderly public spaces. This article provides empirical and conceptual insights into the regulation of coastal freedom camping in New Zealand, drawing on the notion of police power. This form of law is centrally concerned with preventing disruption and disorder in public space, and seeks to advance collective welfare rather than individual rights. The purpose of this article is twofold. First, we consider why and how local governments in New Zealand regulate coastal freedom camping, focusing on a case study of the Coromandel district. Second, we consider how freedom campers understand and experience the regulation of their activities, drawing on a survey of 61 campers in three North Island coastal areas. We find that the policing of freedom camping proceeds through regulation of space, objects and behaviours. Underpinning this approach is an understanding of the activity as inherently problematic. Freedom campers themselves were generally aware of local regulations, but had little experience of enforcement. Most sought to perform camping responsibly, whilst noting that some others required policing.
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B-Trees have been traditionally optimized for I/O performance with disk pages as tree nodes. Recently, researchers have proposed new types of B-Trees optimized for CPU cache performance in main memory environments, where the tree node sizes are one or a few cache lines. Unfortunately, due primarily to this large discrepancy in optimal node sizes, existing disk-optimized B-Trees su er from poor cache performance while cache-optimized B-Trees exhibit poor disk performance. In this paper, we propose fractal prefetching B-Trees (fpB-Trees), which embed \cache-optimized" trees within \disk-optimized" trees, in order to optimize both cache and I/O performance. We design and evaluate two approaches to breaking disk pages into cache-optimized nodes: diskrst and cacherst. These approaches are somewhat biased in favor of maximizing disk and cache performance, respectively, as demonstrated by our results. Both implementations of fpB-Trees achieve dramatically better cache performance than disk-optimized B-Trees: a factor of 1.1{1.8 improvement for search, up to a factor of 4.2 improvement for range scans, and up to a 20-fold improvement for updates. In addition, fpB-Trees accelerate I/O performance for range scans by using jump-pointer arrays to prefetch leaf pages, thereby achieving a speed-up of 2.5{5 on IBM's DB2 Universal Database. This research is supported in part by grants from the National Science Foundation, Microsoft, and Intel.
Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is, tet(K), tet(L), tet(M), tet(O), tet(S), and tet(W), and two with respect to erythromycin, that is, erm(B) and erm(F). The most common resistance genes in the analysed cheeses were tet(S), tet(W), tet(M), and erm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to 10.18log⁡10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions for tet(W)-carrying cheeses, though the similarity of the sequences suggests this tet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants.
Sumitomo electric's navigation systems for private automobiles

The recently developed navigation systems discussed in this paper include location detection using map-matching, map display, and improved man-machine interface functions, and are contained in a stand-alone system installed in passenger cars. The newest system uses a fiber optic gyroscope as a rotation rate sensor, and improved map-matching method to get high accuracy. As to driving guide information, the system can display road information from road side radio beacons, and can play CD-ROM discs based on CDCRAFT which is proposed in Japan as a common standard of CD format and application program for navigation systems.
THOROUGH INSIGHTS BY ENHANCED VISUALIZATION OF FLOW TOPOLOGY

The investigation of flow data can be eased by the visualizati on of topological information about the flow. Especially, when empirical models or numerical results fro m flow simulation are investigated, often the first step of analysis is to search structural elements, like fixed points, separatrices, etc. The work presented in this paper focuses on the visualization of 3D dynamical sy stems (comparable to flow data) on the basis of results which are obtained by automatic analysis of the flo w topology. Fixed points are determined and the Jacobian matrix of the flow is investigated at these point s of phase space to obtain the associated stable and/or unstable invariant sets. Furthermore, this paper pr esents how Poincaré maps are used to visualize structural information about cyclic flow data together with direct visualization cues like stream lines or stream surfaces.
CloudMirror: Application-Aware Bandwidth Reservations in the Cloud

Cloud computing providers today do not offer guarantees for the network bandwidth available in the cloud, preventing tenants from running their applications predictably. To provide guarantees, several recent research proposals offer tenants a virtual cluster abstraction, emulating physical networks. Whereas offering dedicated virtual network abstractions is a significant step in the right direction, in this paper we argue that the abstractions exposed to tenants should aim to model tenant application structures rather than aiming to mimic physical network topologies. The fundamental problem in providing users with dedicated network abstractions is that the communication patterns of real applications do not typically resemble the rigid physical network topologies. Thus, the virtual network abstractions often poorly represent the actual communication patterns, resulting in overprovisioned/wasted network resources and underutilized computational resources. We propose a new abstraction for specifying bandwidth guarantees, which is easy to use because it closely follows application models; our abstraction specifies guarantees as a graph between application components. We then propose an algorithm to efficiently deploy this abstraction on physical clusters. Through simulations, we show that our approach is significantly more efficient than prior work for offering bandwidth guarantees.
Gravitational Lensing by Galaxy Groups in the Hubble Deep Field

We investigate strong lensing of galaxies in the Hubble Deep Field by foreground groups and clusters of galaxies with masses from 1013 to 1015 M☉. Over this mass range, groups with the Navarro, Frenk, & White profile are less efficient than singular isothermal spheres at producing multiple images of galaxies, by factors of 5 × 10-2 to 10-3. This difference highlights the sensitivity of the lensing cross section to the central density profile. Nonetheless, with either profile we find that the expected number of galaxies lensed by groups in the Hubble Deep Field is at most ≲1, consistent with the lack of clearly identified group lens systems.
On using MLP features in LVCSR

One of the major research thrusts in the speech group at ICSI is to use Multi-Layer Perceptron (MLP) based features in automatic speech recognition (ASR). This paper presents a study of three aspects of this effort: 1) the properties of the MLP features which make them useful, 2) incorporating MLP features together with PLP features in ASR, and 3) possible redundancy between MLP features and more conventional system refinements such as discriminative training and system combination. The paper shows that MLP transformations yield variables that have regular distributions, which can be further modified by using logarithm to make the distribution easier to model by a Gaussian-HMM. Two or more vectors of these features can easily be combined without increasing the feature dimension. Recognition results show that MLP features can significantly improve recognition performance in large vocabulary continuous speech recognition (LVCSR) tasks for the NIST 2001 Hub-5 evaluation set with models trained on the Switchboard Corpus, even when discriminative training and system combination are used.
Creases-persevering Mesh Smoothing Based on the Discrete Differential Operators

This paper introduces a new method to mesh smoothing with crease-preserving by using discrete differential Laplacian operators. The eigenfunctions of the Laplace-Beltrami operator are used to define Fourier-like function basis and transform because it is both geometry aware and orthogonal. But the low-pass filters based on Fourier-like methods cannot preserve the creases. This paper proposes a novel approach which can preserve the creases better when filtering, and it can effectively get rid of various of noise in arbitrary 3D meshed surfaces, more over completely prevent the model from shrinking and deforming.
JGromacs: A Java Package for Analyzing Protein Simulations

In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch. ox.ac. uk/jgromacs under a GPLv3 license.
The third wave of cultural psychology-The indigenous movement

The Psychologist Vol 18 No 2 The third wave of cultural psychology The indigenous movement S INCE the end of World War II there have been three large-scale academic movements attempting to incorporate non-Western cultural factors into psychological research: modernisation theory, research on individualism/ collectivism, and the indigenisation movement. These waves in cultural psychology have not risen randomly: what’s fascinating is that they reflect the power structure of the scientific community as well as the power relationships between Western and non-Western countries. This article reviews the main ideas of these three academic movements as well as the sociohistorical background relevant to their incubation, in order to illuminate the epistemological implications of the emergence of the third wave, the indigenous movement. Is the new wave what we have been waiting for, or just more scientific ethnocentrism in disguise?
A SOM-Based Information Organizer for Text and Video Data

We propose an information organizer for e ective clustering and similarity-based retrieval of text and video data. Instead of giving keywords or authoring them, we use a vector space model and DCT image coding in order to extract characteristics of data. Data are clustered by Kohonen's self-organizing map, and the result is visualized in a 3D form. By this, similarity-based retrieval is achieved. We implemented a prototype system and report experimental results. We consider that our system e ectively promotes reuse of distributed text and image data assets.