Miracle-dz/UniFAR-FTUs huggingface dataset:
An Engineered Breast Cancer Model on a Chip to Replicate ECM‐Activation In Vitro during Tumor Progression

In this work, a new model of breast cancer is proposed featuring both epithelial and stromal tissues arranged on a microfluidic chip. The main task of the work is the in vitro replication of the stromal activation during tumor epithelial invasion. The activation of tumor stroma and its morphological/compositional changes play a key role in tumor progression. Despite emerging evidences, to date the activation of tumor stroma in vitro has not been achieved yet. The tumor‐on‐chip proposed in this work is built in order to replicate the features of its native counterpart: multicellularity (tumor epithelial cell and stromal cell); 3D engineered stroma compartment composed of cell‐assembled extracellular matrix (ECM); reliable 3D tumor architecture. During tumor epithelial invasion the stroma displayed an activation process at both cellular and ECM level. Similarly of what repeated in vivo, ECM remodeling is found in terms of hyaluronic acid and fibronectin overexpression in the stroma compartment. Furthermore, the cell‐assembled ECM featuring the stromal tissue, allowed on‐line monitoring of collagen remodeling during stroma activation process via real time multiphoton microscopy. Also, trafficking of macromolecules within the stromal compartment has been monitored in real time.
Individual dopaminergic neurons show raised iron levels in Parkinson disease

Objective: Evidence suggests that abnormal iron metabolism is associated with Parkinson disease (PD), with raised iron levels found in pathologically affected areas in PD. It is unknown if this elevated iron is actually associated with neurons or reactive glia, and we therefore addressed this issue by determining if raised iron was present in single dopaminergic neurons. Methods: We used unfixed frozen sections from postmortem tissue of PD patients and elderly normal individuals to avoid metal contamination and translocation. Levels of iron and other elements were measured using sensitive and specific wavelength dispersive electron probe x-ray microanalysis coupled with cathodoluminescence spectroscopy in individual substantia nigra dopaminergic neurons. Results: We identified raised intraneuronal iron in single defined substantia nigra neurons in PD (mean neuronal iron 2,838 vs 1,611, p < 0.0001) but not in other movement disorders such as Huntington disease. These findings were unrelated to the density of remaining neurons. Conclusions: Primary changes in neuronal iron could lead to neurodegeneration in Parkinson disease.
Transitive Re-identification

Person re-identification accuracy can be significantly improved given a training set that demonstrates changes in appearances associated with the two non-overlapping cameras involved. Here we test whether this advantage can be maintained when directly annotated training sets are not available for all camera-pairs at the site. Given the training sets capturing correspondences between cameras A and B and a different training set capturing correspondences between cameras B and C, the Transitive Re-IDentification algorithm (TRID) suggested here provides a classifier for (A,C) appearance pairs. The proposed method is based on statistical modeling and uses a marginalization process for the inference. This approach significantly reduces the annotation effort inherent in a learning system, which goes down from O(N2) to O(N), for a site containing N cameras. Moreover, when adding camera (N + 1), only one inter-camera training set is required for establishing all correspondences. In our experiments we found that the method is effective and more accurate than the competing camera invariant approach.
Tomographic investigations of temporal variations of the ionospheric electron density and the implied fluxes

A new technique is introduced for determining plasma fluxes using tomographic images of ionospheric electron density. Pairs of images are used to estimate the time derivative of the F‐region electron density in the region of the northern equatorial anomaly at 120°E longitude. Characteristics of temporal variations are described, and two different methods are used to infer electron fluxes from the measured time derivaties. The height‐dependent latitudinally‐averaged vertical flux and a 2D “potential” flux are derived based on reasonable assumed boundary conditions. Examples illustrate that average vertical plasma fluxes in the local morning and evening hours are upward and downward, respectively, with peak magnitudes on the order of 109 cm−2s−1. The 2D plasma fluxes in a meridional cross‐section through the equatorial anomaly are calculated, and clearly illustrate the characteristic flow associated with the equatorial fountain effect.
Effect of earthworm active protein on fibroblast proliferation and its mechanism

Abstract Context: Earthworms have been used as a traditional medicine in China from thousands of years. In recent years, research has demonstrated that earthworm extracts might promote wound healing; however, its mechanism is still unknown. Objective: The study investigates the mechanism and effects of earthworm active protein (EAP), on mouse embryonic fibroblast (NIH/3T3) proliferation. Materials and methods: The effects of earthworm active protein (EAP) in different concentrations (0, 25, 50, 100, 150, and 200 μg/mL) on NIH3T3 cell were detected by the MTT and Brdu incorporation assay (50, 100, and 150 μg/mL). The effects of EAP (37.5, 75, and 150 μg/mL) on the cell cycle were detected by flow cytometry. The cell signaling pathways of EAP-promoting NIH3T3 cell proliferation were studied by the MTT and Western blot by using different signaling pathway inhibitors. Results: The results showed that EAP (50, 100, and 150 μg/mL) could promote NIH3T3 fibroblasts proliferation (36.4 ± 4.4%, 59.1 ± 4.9%, and 71.5 ± 5.7%). The mechanism of EAP promoting NIH3T3 cell proliferation should be as follows: EAP elevated cyclin D1 expression by activating MEK/ERK signaling pathway, and then promoted cell cycle from G1 to S phase, finally caused the proliferation of NIH3T3 cell. PI3K signaling pathway may be the upstream of MEK/ERK signaling pathway. Discussion and conclusion: The study demonstrates that EAP is effective in promoting effects on proliferation and migration activity of NIH3T3 cell, and the proliferation activity of EAP on NIH3T3 cell may be achieved through the PI3K→Rac→PAK→MEK signaling pathway.
Speech Understanding in Open Tasks

The Air Traffic Information Service task is currently used by DARPA as a common evaluation task for Spoken Language Systems. This task is an example of open type tasks. Subjects are given a task and allowed to interact spontaneously with the system by voice. There is no fixed lexicon or grammar, and subjects are likely to exceed those used by any given system. In order to evaluate system performance on such tasks, a common corpus of training data has been gathered and annotated. An independent test corpus was also created in a similar fashion. This paper explains the techniques used in our system and the performance results on the standard set of tests used to evaluate systems.
Modeling the performance impact of hot code misprediction in Cross-ISA virtual machines = : Modelagem do impacto de erros de predição de código quente no desempenho de máquinas virtuais

Maquinas virtuais (MVs) sao sistemas que se propoem a eliminar a incompatibilidade entre duas, em geral diferentes, interfaces e dessa forma habilitar a comunicacao entre diferentes sistemas. Nesse sentido, atuando como mediadores, uma MV esta em um ponto que a permite fomentar o desenvolvimento de solucoes inovadoras para varios problemas. Tais sistemas geralmente utilizam tecnicas de emulacao, por exemplo, interpretacao ou traducao dinâmica de binarios, para executar o codigo da aplicacao cliente. Para determinar qual tecnica de emulacao e a ideal para um trecho de codigo geralmente e necessario que a MV empregue algum tipo de predicao para determinar se o beneficio de compilar o codigo supera os custos. Este problema, na maioria dos casos, resume-se a predizer se o dado trecho de codigo sera frequentemente executado ou nao, problema conhecido pelo nome de Predicao de Codigo Quente. Em geral, se o preditor sinalizar um trecho de codigo como quente, a MV imediatamente toma a decisao de compila-lo. Contudo, um problema surge nesta estrategia, a resposta do preditor e apenas a decisao de uma heuristica e e, portanto, suscetivel a erros. Quando o preditor sinaliza como quente um trecho de codigo que nao sera frequentemente executado, ou seja, um codigo que de fato e "frio", ele esta fazendo uma predicao erronea de codigo quente. Quando uma predicao incorreta e feita, ocorre que a tecnica de emulacao que a MV utilizara para emular o trecho de codigo nao compensara o seu custo e, portanto a MV gastara mais tempo executando o seu proprio codigo do que o codigo da aplicacao cliente. Neste trabalho, foi avaliado o impacto de predicoes incorretas de codigo quente no desempenho de MVs emulando varios tipos de aplicacoes. Na analise realizada foi avaliado o preditor de codigo quente baseado em limiar, uma tecnica frequentemente utilizada para identificar regioes de codigo que serao frequentemente executadas. Para fazer esta analise foi criado um modelo matematico para simular o comportamento de tal preditor e a partir deste modelo uma serie de resultados puderam ser explorados. Inicialmente e mostrado que este preditor frequentemente erra a predicao e, como consequencia, o tempo gasto fazendo compilacoes torna-se o maior componente do tempo de execucao da MV. Tambem e mostrado como diferentes limiares de predicao afetam o numero de predicoes incorretas e qual o impacto disto no desempenho da MV. Tambem sao apresentados resultados indicando qual o impacto do custo de compilacao, traducao e velocidade do codigo traduzido no desempenho da MV. Por fim e mostrado que utilizando apenas o conjunto de aplicacoes do SPEC CPU 2006 para avaliar o desempenho de MVs que utilizam o preditor de codigo quente baseado em limiar pode levar a resultados imprecisos. Abstract
CriterionSM Online Essay Evaluation: An Application for Automated Evaluation of Student Essays

This paper describes a deployed educational technology application: the Criterion SM Online Essay Evaluation Service, a web-based system that provides automated scoring and evaluation of student essays. Criterion has two complementary applications: E-rater®, an automated essay scoring system and Critique Writing Analysis Tools, a suite of programs that detect errors in grammar, usage, and mechanics, that identify discourse elements in the essay, and that recognize elements of undesirable style. These evaluation capabilities provide students with feedback that is specific to their writing in order to help them improve their writing skills. Both applications employ natural language processing and machine learning techniques. All of these capabilities outperform baseline algorithms, and some of the tools agree with human judges as often as two judges agree with each other.
MULTIMODAL TRIGGERS FOR AUTOMATED FILTERING AND REACTIVITY BASED ON WWW CONTENT

We describe a multimodal analysis based automated triggering mechanism for automated filtering and reactivity based on the content of multiple multimedia channels over the World Wide Web. The trigger description language supports complex conditions connected through Boolean operators (logical OR, logical AND, and negation), temporal and frequency of occurrence constraints and actions. A trigger can be placed either at the client end or at the server end. We present a grammar for an XML based trigger description language, and it’s corresponding implementation. Performance analysis has been presented.
RNA trafficking and stabilization elements associate with multiple brain proteins

Two of the best understood somatic cell mRNA cytoplasmic trafficking elements are those governing localization of β-actin and myelin basic protein mRNAs. These cis-acting elements bind the trans-acting factors fibroblast ZBP-1 and hnRNP A2, respectively. It is not known whether these elements fulfil other roles in mRNA metabolism. To address this question we have used Edman sequencing and western blotting to identify six rat brain proteins that bind the β-actin element (zipcode). All are known RNA-binding proteins and differ from ZBP-1. Comparison with proteins that bind the hnRNP A2 and AU-rich response elements, A2RE/A2RE11 and AURE, showed that AURE and zipcode bind a similar set of proteins that does not overlap with those that bind A2RE11. The zipcode-binding protein, KSRP, and hnRNP A2 were selected for further study and were shown by confocal immunofluorescence microscopy to have similar distributions in the central nervous system, but they were found in largely separate locations in cell nuclei. In the cytoplasm of cultured oligodendrocytes they were segregated into separate populations of cytoplasmic granules. We conclude that not only may there be families of trans-acting factors for the same cis-acting element, which are presumably required at different stages of mRNA processing and metabolism, but independent factors may also target different and multiple RNAs in the same cell.
Variable distraction 1 Running head : VARIABLE DISTRACTION Oscillating distraction intervals in free recall : A test of contextual retrieval theory

The contiguity effect, the finding that participants organize recalled items in terms of their temporal position on a study list, is a near-ubiquitous feature of studies of free recall. The robustness of this effect to substantial inter-item distraction is thought to reflect the utilization of a retrieval cue that changes slowly as the participant studies items, as well as when they process the distraction events, as described by retrieved-context theories of human memory. By these theories, when studied items are surrounded by equally lengthed periods of inter-item distraction, this does not change the relative likelihood of recalling the surrounding items, causing the contiguity effect to have the same shape as when there is no inter-item distraction. We test this theory by presenting participants with study lists with uneven distraction intervals surrounding the studied material, and find that, in accordance with retrieved-context theories, this experimental manipulation alters the shape of the contiguity effect. An analysis of the effect of temporal isolation of particular items on the memorability of the studied material allows us to contrast the predictions of retrieved-context theories with those of temporal distinctiveness theories. We find that temporally isolated items are less memorable than items with close temporal neighbors, which goes against the predictions of temporal distinctiveness theories but is in accord with retrieved-context theories. Variable distraction 3 Oscillating distraction intervals in free recall: A test of contextual retrieval theory
Regulation of the Bfa 1 p – Bub 2 p complex at spindle pole bodies by the cell cycle phosphatase Cdc 14 p

he budding yeast mitotic exit network (MEN) is a GTPase-driven signal transduction cascade that controls the release of the phosphatase Cdc14p from the nucleolus in anaphase and thereby drives mitotic exit. We show that Cdc14p is partially released from the nucleolus in early anaphase independent of the action of the MEN components Cdc15p, Dbf2p, and Tem1p. Upon release, Cdc14p binds to the spindle pole body (SPB) via association with the Bfa1p–Bub2p GTPase activating protein complex, which is known to regulate the activity of the G protein Tem1p. Cdc14p also interacts with this GTPase. The associT ation of the MEN component Mob1p with the SPB acts as a marker of MEN activation. The simultaneous binding of Cdc14p and Mob1p to the SPB in early anaphase suggests that Cdc14p initially activates the MEN. In a second, later step, which coincides with mitotic exit, Cdc14p reactivates the Bfa1p–Bub2p complex by dephosphorylating Bfa1p. This inactivates the MEN and displaces Mob1p from SPBs. These data indicate that Cdc14p activates the MEN in early anaphase but later inactivates it through Bfa1p dephosphorylation and so restricts MEN activity to a short period in anaphase.
Reliability of 51Cr-EDTA plasma and urinary clearance as a measure of residual renal function in dialysis patients

Abstract Purpose: In dialysis patients, longer survival is associated with a higher residual renal function. Randomized controlled trials are conducted to clarify how residual renal function can be preserved. However, existing methods for measuring residual renal function are uncertain and there is a need for establishing a standard for measurements of glomerular filtration rate (GFR) in dialysis patients. Methods: 51Cr-EDTA clearances in plasma, urine, and dialysate were evaluated in a sample of 12 hemodialysis and 12 peritoneal dialysis patients. The patients’ condition was generally stable, and all patients were investigated twice within 4–10 days. Results: Plasma clearances of 51Cr-EDTA for all patients ranged between 2.1 and 30.8 mL/min/1.73m2, whereas urinary 51Cr-EDTA clearances ranged from 0.7–20.0 mL/min/1.73m2. This difference was statistically significant (p < 0.001). Week-to-week reproducibility expressed as coefficients of variation were below or equal to 10% for plasma clearances and 13% for urinary clearances in hemodialysis patients and 14% in peritoneal dialysis patients. Conclusions: This study demonstrated a difference between 51Cr-EDTA plasma and urinary clearances in dialysis patients. Plasma clearance of 51Cr-EDTA had the best reproducibility. For repeated measurements as in clinical prospective trials, we recommend 51Cr-EDTA plasma clearance based on blood sampling at 5 + 24 hours with subtraction of 51Cr-EDTA dialysate clearance in peritoneal dialysis patients. Further studies are needed to corroborate our findings.
Le collectif face au big data : interprétation partagée et retro-validation des données LiDAR du site d'El Infiernillo, Michoacán, Mexique

L'obtention en 2015 d'une couverture LiDAR (Light Detection and RAnging) de l'integralite du complexe geologique du Malpais de Zacapu, dans le Centre-Ouest Mexicain, a radicalement transforme les modalites d'etude de ce secteur de Mesoamerique. A l'image des experiences similaires menees dans le Bassin de Patzcuaro ou dans la region maya, l'acquisition de donnees LiDAR confronte l'archeologue a de nombreuses reconfigurations methodologiques et paradigmatiques : la chaine operatoire de son travail, en particulier de son travail de terrain peut etre modifiee. Par ailleurs, la masse de donnees a stocker, gerer, analyser, est radicalement multipliee. Des dispositifs et strategies de traitement adaptes doivent, face a cela, etre conceptualises et developpes. Enfin, des tests approfondis et des retro-analyses doivent etre menes pour valider non seulement l'utilisation de la donnee LiDAR, mais aussi les outils de recherche construits dans ce cadre. En partant de donnees acquises et d'interpretations realisees au prealable dans le cadre d'operations de terrain "classiques" et en nous basant sur un cas d'etude, le site archeologique d'El Infiernillo, nous discutons des potentialites des plateformes de traitement cartographiques collaboratives et de la gestion des donnees « tele-interpretees ».
How to Lose Confidence: Probabilistic Linear Machines for Multiclass Classification

In this paper we propose a novel multiclass classifier called the probabilistic linear machine (PLM) which overcomes the low-entropy problem of exponential-based classifiers. Although PLMs are linear classifiers, we use a careful design of the parameters matched with weak requirements over the features to output a true probability distribution over labels given an input instance. We cast the discriminative learning problem as linear programming, which can scale up to large problems on the order of millions of training samples. Our experiments on phonetic classification show that PLM achieves high entropy while maintaining a comparable accuracy to other state-of-the-art classifiers.
TEMPeRA: TEmplate massively PaRAllel library for efficient n-dimensional signal processing

We present TEMPeRA: a C++ library for efficient parallel signal processing, with a focus on image deconvolution. TEMPeRA makes porting new algorithms from MATLAB to C++ easier than with the conventional methods. The library provides a class to describe a signal, with main point-wise algebraic operations, that is compatible with standard library generic algorithms. Interface for linear operators is also provided, suitable for modeling the blurring effect introduced by acquisition devices, such as telescopes or microscopes. Both classes defined in the library can exploit either CPU or GPU, using CUDA: this allows the end user to write device independent code. Moreover, thanks to policy-based template design, support for different architectures is introduced. The library is then exploited for the implementation of Richardson-Lucy deconvolution algorithm. Benchmark results shows remarkable speedup when comparing serial (CPU) code and parallel (CUDA) implementation.
Graph Zeta Function in the Bethe Free Energy and Loopy Belief Propagation

We propose a new approach to the analysis of Loopy Belief Propagation (LBP) by establishing a formula that connects the Hessian of the Bethe free energy with the edge zeta function. The formula has a number of theoretical implications on LBP. It is applied to give a sufficient condition that the Hessian of the Bethe free energy is positive definite, which shows non-convexity for graphs with multiple cycles. The formula clarifies the relation between the local stability of a fixed point of LBP and local minima of the Bethe free energy. We also propose a new approach to the uniqueness of LBP fixed point, and show various conditions of uniqueness.
Fast Snippet Generation Based on CPU-GPU Hybrid System

As an important part of searching result presentation, query-biased document snippet generation has become a popular method of search engines that makes the result list more informative to users. Generating a single snippet is a lightweight task. However, it will be a heavy workload to generate multiple snippets of multiple documents as the search engines need to process large amount of queries per second, and each result list usually contains several snippets. To deal with this heavy workload, we propose a new high-performance snippet generation approach based on CPU-GPU hybrid system. Our main contribution of this paper is to present a parallel processing stream for large-scale snippet generation tasks using GPU. We adopt a sliding document segmentation method in our approach which costs more computing resources but can avoid the common defect that the high relevant fragment may be cut off. The experimental results show that our approach gains a speedup of nearly 6 times in average process time compared with the baseline approach-Highlighter.