Miracle-dz/UniFAR-FTUs huggingface dataset:
EZH2 Is Overexpressed in BRCA1-like Breast Tumors and Predictive for Sensitivity to High-Dose Platinum-Based Chemotherapy

Purpose: BRCA1-deficient breast cancers carry a specific DNA copy-number signature (“BRCA1-like”) and are hypersensitive to DNA double-strand break (DSB) inducing compounds. Here, we explored whether (i) EZH2 is overexpressed in human BRCA1-deficient breast tumors and might predict sensitivity to DSB-inducing drugs; (ii) EZH2 inhibition potentiates cisplatin efficacy in Brca1-deficient murine mammary tumors. Experimental Design: EZH2 expression was analyzed in 497 breast cancers using IHC or RNA sequencing. We classified 370 tumors by copy-number profiles as BRCA1-like or non-BRCA1–like and examined its association with EZH2 expression. Additionally, we assessed BRCA1 loss through mutation or promoter methylation status and investigated the predictive value of EZH2 expression in a study population of breast cancer patients treated with adjuvant high-dose platinum-based chemotherapy compared with standard anthracycline-based chemotherapy. To explore whether EZH2 inhibition by GSK126 enhances sensitivity to platinum drugs in EZH2-overexpressing breast cancers we used a Brca1-deficient mouse model. Results: The highest EZH2 expression was found in BRCA1-associated tumors harboring a BRCA1 mutation, BRCA1-promoter methylation or were classified as BRCA1 like. We observed a greater benefit from high-dose platinum-based chemotherapy in BRCA1-like and non-BRCA1–like patients with high EZH2 expression. Combined treatment with the EZH2 inhibitor GSK126 and cisplatin decreased cell proliferation and improved survival in Brca1-deficient mice in comparison with single agents. Conclusions: Our findings demonstrate that EZH2 is expressed at significantly higher levels in BRCA1-deficient breast cancers. EZH2 overexpression can identify patients with breast cancer who benefit significantly from intensified DSB-inducing platinum-based chemotherapy independent of BRCA1-like status. EZH2 inhibition improves the antitumor effect of platinum drugs in Brca1-deficient breast tumors in vivo.
A National Study of the Consequences of Fire and Fire Surrogate Treatments

Other Contributors/ Collaborators: Tony Caprio (Fire Ecologist, Sequoia NP), Bill Kaage (Fire Management Specialist, Sequoia NP, MaryBeth Keifer (Ecologist, Sequoia NP), Steve Zack (Wildlife Ecologist, Wildlife Conservation Society), Kerry Farris (Wildlife Ecologist, Wildlife Conservation Society), Philip Rundel (Professor, University of California Los Angeles), and Jamie Barbour (Wood Scientist, Portland Forestry Sciences Laboratory)
Professional Rigor, Public Engagement and Judicial Review: A Proposal for Enhancing the Validity of Education Adequacy Studies

Background/Context In recent years, state legislatures, state education departments, and advocacy groups in over 30 states have sponsored education adequacy studies, which aim to determine objectively the amount of funding needed to provide all students a meaningful opportunity for an adequate education. Not surprisingly, because of their growing influence on funding decisions, these studies have now become the subject of critical commentary and judicial scrutiny, and serious questions have arisen about the validity of the methodologies used in some of the studies. By setting out to determine objectively the resource levels needed to provide all students with an adequate education—and by doing so through relatively open and transparent processes— the contemporary adequacy cost studies are vast improvements over the ad-hoc political deal-making processes of the past. Nevertheless, the validity and the reliability of these methodologies can be improved. Purpose/Objective/Research Question/Focus of Study This article provides the first detailed analysis of judicial critiques of the state of the art of “costing out” studies in order to recommend improvements to the current practice of costing-out educational adequacy. Research Design The article engages in an extensive review of judicial critiques of adequacy cost studies, literature critiquing adequacy cost studies, and the adequacy cost studies themselves, in order to identify the best and worst practices in the field. Conclusions/Recommendations Based on these critiques, the article recommends explicit articulation of the premises behind the adoption of particular outcome standards, more precise means for identifying the extent to which students with special needs require extra resources, specific mechanisms to minimize political bias and political manipulations, and the use of “quality education models” to integrate efficiency and accountability considerations within the basic cost analysis. In addition, more extensive public engagement and continuing judicial oversight will be necessary to ensure the credibility and the legitimacy of the ultimate judgments that result from these studies.
GTM-UVigo System for Multimodal Person Discovery in Broadcast TV Task at MediaEval 2016

In this paper, we present the system developed by GTM-UVigo team for the Multimedia Person Discovery in Broad-cast TV task at MediaEval 2016. The proposed approach consists in a novel strategy for person discovery which is not based on speaker and face diarisation as in previous works. In this system, the task is approached as a person recognition problem: there is an enrolment stage, where the voice and face of each discovered person are detected and, for each shot, the most suitable voice and face are assigned using the i-vector paradigm. These two biometric modalities are combined by decision fusion.
PEP-1-GSTpi protein enhanced hippocampal neuronal cell survival after oxidative damage

Reactive oxygen species generated under oxidative stress are involved in neuronal diseases, including ischemia. Glutathione S-transferase pi (GSTpi) is a member of the GST family and is known to play important roles in cell survival. We investigated the effect of GSTpi against oxidative stress-induced hippocampal HT-22 cell death, and its effects in an animal model of ischemic injury, using a cell-permeable PEP-1-GSTpi protein. PEP-1-GSTpi was transduced into HT-22 cells and significantly protected against H2O2-treated cell death by reducing the intracellular toxicity and regulating the signal pathways, including MAPK, Akt, Bax, and Bcl-2. PEP-1-GSTpi transduced into the hippocampus in animal brains, and markedly protected against neuronal cell death in an ischemic injury animal model. These results indicate that PEP-1-GSTpi acts as a regulator or an antioxidant to protect against oxidative stress-induced cell death. Our study suggests that PEP-1-GSTpi may have potential as a therapeutic agent for the treatment of ischemia and a variety of oxidative stress-related neuronal diseases. [BMB Reports 2016; 49(7): 382-387]
Effect of age on body water and resting metabolic rate.

BACKGROUND We previously reported that differences in fat-free mass (FFM) estimated by isotope dilution of 18O-labeled water could not fully account for lower resting metabolic rates (RMR) in old men and women compared to RMR in young men. METHODS Since age-related changes in the distribution of water between extracellular and intracellular spaces could lead to overestimation of FFM in the old, we reanalyzed our data using estimates for total body and intracellular water (TBW and ICW, respectively) derived from published equations and included data from adolescent boys and girls studied under similar conditions. RESULTS In both sexes, the age-related reduction in RMR remained significant after adjustment for estimated body water compartments (p < .05). While adjusted RMR differed in boys and girls (p < .0001), it did not in old men and women (p = .15). CONCLUSION We conclude that aging per se reduces RMR in lean tissue, a difference which cannot be fully explained by changes in body water or its distribution. Investigators should be cautious when selecting models and equations to estimate body water compartments.
Energy-efficient network design via modelling: optimal designing point for energy, reliability, coverage and end-to-end delay

Considering that practical wireless sensor networks are mostly built upon energy-constrained sensor nodes, network lifetime becomes a key deployment factor for sustainability of such networks initiating an attempt for prolonging the lifetime. Adopting a new multi-mode switching protocol for sensor nodes between active and sleep states, in this study, the authors propose a new mathematical method using an embedded simulation-based computing of an energy-efficient strategy performance metric to maintain resiliency of the network against side effects appearing in duty-cycling protocols. Here, the authors use a Monte Carlo simulation to estimate network reliability. Then the proposed mathematical model enables us to build a decision for optimised performance upon trade-offs between consumed energy, reliability, coverage intensity and end-to-end delays by locating a network's operational points. The authors show the trade-off operational significance of the model against the percentage of sleeping probability via some design factors including figure of merit.
Compressing Grasping Experience into a Dictionary of Prototypical Grasp-predicting Parts

We present a real-world robotic agent that is capable of transferring grasping strategies across objects that share similar parts. The agent transfers grasps across objects by identifying, from examples provided by a teacher, parts by which objects are often grasped in a similar fashion. It then uses these parts to identify grasping points onto novel objects. Because most human environments make it infeasible to pre-program grasping behaviors for every object the robot might encounter, grasping novel objects is a key issue in human-friendly robotics. Recent approaches to grasping novel objects aim at devising a direct mapping from visual features to grasp parameters. A central question in such approaches is what visual features to use. Some authors have shown that grasps can be computed from local visual features [3]. However, local features suffer from poor geometric resolution, which makes it difficult to accurately compute the 6D pose of a gripper. By contrast, using object parts as features allows robots to compute grasps of high geometric accuracy [1], [2], [4]. We present a method that allows a robot to learn to formulate grasp plans from visual data obtained from a 3D sensor. Our method relies on the identification of prototypical parts by which objects are often grasped. To this end, we provide the robot with means of identifying, from a set of grasp examples, the 3D shape of parts that are recurrently observed within the manipulator during the grasps. Our approach effectively compresses the training data, generating a dictionary of prototypical parts that is an order of magnitude smaller than the training dataset. As prototypical parts are extracted from grasp examples, each of them automatically inherits a grasping strategy that parametrizes (1) the position and orientation of the manipulator with respect to the part, and (2) the finger preshape, i.e., the configuration in which fingers should be set prior to grasping. When a novel object appears, the robot tries to fit the prototypical parts to a snapshot that partially captures the object. The grasp associated to the part that best fits the snapshot can be executed to manipulate the object. A key aspect of our work is that the shape and the spatial extent (or size) of the prototypes generated by our method directly result from
Implementation and Application of a Binaural Hearing Model to the Objective Evaluation of Spatial Impression

A binaural hearing model has been developed over a number of years that predicts the perceived width and position of sounds, over frequency and over time. The most appropriate methods for applying this model to evaluations of spatial impression are considered, including suitable test signals. Examples of a range of measurements are shown in a range of situations.
Mechanism of spontaneous excitability in human embryonic stem cell derived cardiomyocytes

Human embryonic stem cell‐derived cardiomyocytes (hES‐CMs) are thought to recapitulate the embryonic development of heart cells. Given the exciting potential of hES‐CMs as replacement tissue in diseased hearts, we investigated the pharmacological sensitivity and ionic current of mid‐stage hES‐CMs (20–35 days post plating). A high‐resolution microelectrode array was used to assess conduction in multicellular preparations of hES‐CMs in spontaneously contracting embryoid bodies (EBs). TTX (10 μm) dramatically slowed conduction velocity from 5.1 to 3.2 cm s−1 while 100 μm TTX caused complete cessation of spontaneous electrical activity in all EBs studied. In contrast, the Ca2+ channel blockers nifedipine or diltiazem (1 μm) had a negligible effect on conduction. These results suggested a prominent Na+ channel current, and therefore we patch‐clamped isolated cells to record Na+ current and action potentials (APs). We found for isolated hES‐CMs a prominent Na+ current (244 ± 42 pA pF−1 at 0 mV; n= 19), and a hyperpolarization‐activated current (HCN), but no inward rectifier K+ current. In cell clusters, 3 μm TTX induced longer AP interpulse intervals and 10 μm TTX caused cessation of spontaneous APs. In contrast nifedipine (Ca2+ channel block) and 2 mm Cs+ (HCN complete block) induced shorter AP interpulse intervals. In single cells, APs stimulated by current pulses had a maximum upstroke velocity (dV/dtmax) of 118 ± 14 V s−1 in control conditions; in contrast, partial block of Na+ current significantly reduced stimulated dV/dtmax (38 ± 15 V s−1). RT‐PCR revealed NaV1.5, CaV1.2, and HCN‐2 expression but we could not detect Kir2.1. We conclude that hES‐CMs at mid‐range development express prominent Na+ current. The absence of background K+ current creates conditions for spontaneous activity that is sensitive to TTX in the same range of partial block of NaV1.5; thus, the NaV1.5 Na+ channel is important for initiating spontaneous excitability in hES‐derived heart cells.
Tumor Necrosis Factor Death Receptor Signaling Cascade Is Required for Amyloid-β Protein-Induced Neuron Death

Tumor necrosis factor type I receptor (TNFRI), a death receptor, mediates apoptosis and plays a crucial role in the interaction between the nervous and immune systems. A direct link between death receptor activation and signal cascade-mediated neuron death in brains with neurodegenerative disorders remains inconclusive. Here, we show that amyloid-β protein (Aβ), a major component of plaques in the Alzheimer's diseased brain, induces neuronal apoptosis through TNFRI by using primary neurons overexpressing TNFRI by viral infection or neurons from TNFRI knock-out mice. This was mediated via alteration of apoptotic protease-activating factor (Apaf-1) expression that in turn induced activation of nuclear factor κB (NF-κB). Aβ-induced neuronal apoptosis was reduced with lower Apaf-1 expression, and little NF-κB activation was found in the neurons with mutated Apaf-1 or a deletion of TNFRI compared with the cells from wild-type (WT) mice. Our studies suggest a novel neuronal response of Aβ, which occurs through a TNF receptor signaling cascade and a caspase-dependent death pathway.
Composition, Cooperation, and Coordination of Computational Systems

A system model is developed where the criterion to par- tition the world into a system and a rest is based on the functional relation between its states. This approach implies that the gestalt of systems becomes very dynamic. Especially interactions between systems may create temporary super systems "on the fly". The reference to the function notion establishes the link to computation. It is shown that being computable is a system property which is compositional in an ab- stract mathematical sense but is, because of recursion, emergent from a computational point of view. Based on the distinction between the intended determinism versus non- determinism of the interaction, two classes of system interactions are distinguished: composition and cooperation. Composition means that by interaction super systems are created and the interacting systems become subsystems. Cooperation means that systems sensibly interact loosely without creating any identifiable super system function and therefore without super system creation from the perspective of the interacting systems. Cooperative system interactions are described with the help of the pro- tocol notion based on shared states, interpreted as the stateful exchange of characters via Shannon channels between roles - the projection of systems onto the interaction channels. It is shown that roles can be in- ternally coordinated by a set of rules, leading to a very flexible process notion which unfolds its full potential only in a new type of execution environment capable of executing spontaneous transitions. The system model has immediate implications for componentization which can be viewed as an attempt to either hide functional recursion and provide only functionality whose composition behavior is easy to un- derstand, or to provide loosely coupled interactions via protocols. To be complete, component models should therefore at least support three gen- eral classes of components: one for loose coupling, one for hierarchical composition, and one for pipes.
Efficient computation of controller partitions in multi-parametric programming

The off-line solution to optimal control problems for linear or piecewise-affine systems with constraints has garnered much attention because the on-line implementation can be realized with a simple look-up table. Specifically, multi-parametric programming techniques can be utilized to compute a piecewise-affine feedback law off-line. Even though the computation is performed off-line, the necessary computation time may easily become excessive for larger problems. This paper identifies the computation of minimal representations of polytopes as a key driver for complexity and presents an efficient method for reducing the associated computation cost. The method utilizes bounding-boxes and ray-shooting to discard redundant hyper-planes efficiently. A case study demonstrates the computational advantages.
Membrane Filter Method for Enumeration of Acinetobacter calcoaceticus from Environmental Waters

A membrane filter method was developed and evaluated for the quantitative recovery of Acinetobacter calcoaceticus from environmental waters. The procedure utilized a mineral medium, with sodium acetate and potassium nitrate as the carbon and nitrogen sources, respectively. Formic acid was included to enhance the recovery of A. calcoaceticus and to inhibit background growth. The medium was incubated for 46 h at 30°C, after which fermentation and cytochrome oxidase tests were performed on the colonies as they appeared on the membrane. Background microbial growth decreased on the average by 1.77 orders of magnitude. An essentially quantitative recovery relative to that on nutrient agar spread plates was obtained from freshly prepared suspensions of eight A. calcoaceticus strains in filter-sterilized pond water and from suspensions of five of the strains held for up to 96 h in filter-sterilized pond water at 15 and 22°C. Markedly reduced relative recoveries were obtained with the three remaining strains. However, these three strains, in contrast to the first five, not only did not grow, but also decreased in number in the eutrophic, filter-sterilized pond water. The confirmation rate of presumptive A. calcoaceticus colonies was 95%, whereas 8% of the presumptively negative colonies were A. calcoaceticus. The precision of the method did not exceed that expected from random error alone. Densities of A. calcoaceticus in freshwaters ranged from <1 to 7.9 × 104 organisms per 100 ml and were about 106 organisms per 100 ml in raw sewage.
Evaluation of TnT Tagger for Spanish

Part of speech (POS) tagger is a necessary module in many natural language text processing tasks. A POS tagger is a program that accepts an unprepared raw text in input and to each word adds a tag specifying its grammatical properties, such as part of speech, number, person, etc. One of popular POS taggers - TnT tagger - has been extensively tested for English and some other languages. This paper reports on its evaluation for Spanish language. Error analysis is reported, explaining how some specific features of Spanish language affect tagger performance. It is reported that on Spanish texts TnT shows overall tagging accuracy between 92.5% and 95.84%, specifically, between 95.47% and 98.56% on known words and between 75.57% and 83.49% on unknown words. Results show that TnT has reached a good level of maturity and is helpful enough for NLP tasks.
Research on GA-SVM Based Head-Motion Classification via Mechanomyography Feature Analysis

This study investigated classification of six types of head motions using mechanomyography (MMG) signals. An unequal segmenting algorithm was adopted to segment the MMG signals generated by head motions. Three types of features (time domain, time-frequency domain and nonlinear dynamics) were extracted to construct five feature sets as candidate datasets for classification analysis. Genetic algorithm optimized support vector machine (GA-SVM) was used to classify the MMG signals. Three different kernel functions, different combinations of feature sets, different number of signal channels and training samples were selected for comparative analysis to evaluate the classification accuracy. Experimental results showed that the classifier had the best overall classification accuracy when using the radial basis function (RBF). Any combination of three different types of feature sets guaranteed an average accuracy of over 80%. In the case of the best combination (feature set 2 + 3 + 5), the classification accuracy was up to 88.2%. Using four channels to acquire MMG signal and no less than 60 training samples can assure a satisfactory classification accuracy.
Dynamic hierarchical Bayesian network for Arabic handwritten word recognition

This paper presents a new probabilistic graphical model used to model and recognize words representing the names of Tunisian cities. In fact, this work is based on a dynamic hierarchical Bayesian network. The aim is to find the best model of Arabic handwriting to reduce the complexity of the recognition process by permitting the partial recognition. Actually, we propose a segmentation of the word based on smoothing the vertical histogram projection using different width values to reduce the error of segmentation. Then, we extract the characteristics of each cell using the Zernike and HU moments, which are invariant to rotation, translation and scaling. Our approach is tested using the IFN / ENIT database, and the experiment results are very promising.