Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous Analysis of SEPT9 Promoter Methylation Status, Micronuclei Frequency, and Folate-Related Gene Polymorphisms: The Potential for a Novel Blood-Based Colorectal Cancer Biomarker

One challenge in colorectal cancer (CRC) is identifying novel biomarkers to be introduced in screening programs. The present study investigated the promoter methylation status of the SEPT9 gene in peripheral blood samples of subjects’ positive fecal occult blood test (FOBT). In order to add new insights, we investigated the association between SEPT9 promoter methylation and micronuclei frequency, and polymorphisms in the folate-related pathway genes. SEPT9 promoter methylation, micronuclei frequency, and genotypes were evaluated on 74 individuals’ FOBT positive. Individuals were subjected to a colonoscopy that provided written informed consent for study participation. SEPT9 promoter methylation status was significantly lower in the CRC group than controls (p = 0.0006). In contrast, the CaCo2 cell-line, analyzed as a tissue specific model of colon adenocarcinoma, showed a significantly higher percentage of SEPT9 promoter methylation compared to the CRC group (p < 0.0001). Linear regression analysis showed an inverse correlation between micronuclei frequency and the decrease in the methylation levels of SEPT9 promoter region among CRC patients (β = −0.926, p = 0.0001). With regard to genotype analysis, we showed the involvement of the DHFR polymorphism (rs70991108) in SEPT9 promoter methylation level in CRC patients only. In particular, the presence of at least one 19 bp del allele significantly correlates with decreased SEPT9 promoter methylation, compared to the 19 bp ins/ins genotype (p = 0.007). While remaining aware of the strengths and limitations of the study, this represents the first evidence of a novel approach for the early detection of CRC, using SEPT9 promoter methylation, micronuclei frequency and genotypes, with the potential to improve CRC risk assessment.
Boosting Static Analysis of Android Apps through Code Instrumentation

Static analysis has been applied to dissect Android apps for many years. The main advantage of using static analysis is its efficiency and entire code coverage characteristics. However, the community has not yet produced complete tools to perform in-depth static analysis, putting users at risk to malicious apps. Because of the diverse challenges caused by Android apps, it is hard for a single tool to efficiently address all of them. Thus, in this work, we propose to boost static analysis of Android apps through code instrumentation, in which the knotty code can be reduced or simplified into an equivalent but analyzable code. Consequently, existing static analyzers, without any modification, can be leveraged to perform extensive analysis, although originally they cannot. Previously, we have successfully applied instrumentation for two challenges of static analysis of Android apps: Inter-Component Communication (ICC) and Reflection. However, these two case studies are implemented separately and the implementation is not reusable, letting some functionality, that could be reused from one to another, be reinvented and thus lots of resources are wasted. To this end, in this work, we aim at providing a generic and non-invasive approach for existing static analyzers, enabling them to perform more broad analysis.
Cinematographic rules applied to a camera network

We present a camera network system consisting of several modules of 2-3 low end cameras attached to one computer. It is not possible for a human to observe all the information coming from such a network simultaneously. Our system is designed to select the best viewpoint for each part of the video sequence, thus automatically creating one real-time video stream that contains the most important data. It acts as a combination of a director and a cameraman. Cinematography developed its own terminology, techniques and rules, how to make a good movie. We illustrate here some of these techniques and how they can be applied to a camera network, to solve the best viewpoint selection problem. Our system consists of only fixed cameras, but the output is not constrained to already existing views. A virtual zoom can be applied to select only a part of the view. We propose a view interpolation algorithm which makes it possible to create new intermediate views from the existing camera images. The combination of all these techniques gathers information from a complete camera network and produces one attractive real-time video stream. The resulting video can typically be used for telepresence applications or as a documentary or instruction video.
Experimental Branch Retinal Vein Occlusion Induces Upstream Pericyte Loss and Vascular Destabilization

Aims Branch retinal vein occlusion (BRVO) leads to extensive vascular remodeling and is important cause of visual impairment. Although the vascular morphological changes following experimental vein occlusion have been described in a variety of models using angiography, the underlying cellular events are ill defined. Methods and Results We here show that laser-induced experimental BRVO in mice leads to a wave of TUNEL-positive endothelial cell (EC) apoptosis in the upstream vascular network associated with a transient edema and hemorrhages. Subsequently, we observe an induction of EC proliferation within the dilated vein and capillaries, detected by EdU incorporation, and the edema resolves. However, the pericytes of the upstream capillaries are severely reduced, which was associated with continuing EC apoptosis and proliferation. The vascular remodeling was associated with increased expression of TGFβ, TSP-1, but also FGF2 expression. Exposure of the experimental animals to hypoxia, when pericyte (PC) dropout had occurred, led to a dramatic increase in endothelial cell proliferation, confirming the vascular instability induced by the experimental BRVO. Conclusion Experimental BRVO leads to acute endothelial cells apoptosis and increased permeability. Subsequently the upstream vascular network remains destabilized, characterized by pericyte dropout, un-physiologically high endothelial cells turnover and sensitivity to hypoxia. These early changes might pave the way for capillary loss and subsequent chronic ischemia and edema that characterize the late stage disease.
Effective exploitation of a zero overhead loop buffer

A Zero Overhead Loop Buffer (ZOLB) is an architectural feature that is commonly found in DSP processors. This buffer can be viewed as a compiler managed cache that contains a sequence of instructions that will be executed a specified number of times. Unlike techniques such as loop unrolling, a loop buffer is a hardware technique that can be used to minimize loop overhead without the penalty of increasing code size. In addition, a ZOLB also requires relatively little space and power, which are both important considerations for most DSP applications. This paper describes strategies for generating code to effectively use a ZOLB. The authors have found that many common improving transformations used by optimizing compilers to improve code on conventional architectures are shown (1) to allow more loops to be placed in a ZOLB and (2) to further reduce loop overhead of the loops placed in a ZOLB. The results given in this paper demonstrate that this architectural feature can often be exploited with substantial improvements in execution time and slight reductions in code size.
Planning for change: a reconfiguration language for distributed systems

In order to help programmers achieve greater leverage of emerging reconfiguration mechanisms, we are studying notations for users to express reconfiguration plans. These plans direct how a running distributed application would be changed, based upon recognition of events from either the application itself or its environment. Our work to date in this area is embodied in a simple system called Clipper. Based upon C++, Clipper provides a way for programmers to express plans, that are then used to automatically generate the run time mechanisms needed to validly reflect the programmer's rules for change in the application. This paper presents a description of our language in its current form, along with requirements that led up to it. <<ETX>>
More Than Mentors: Principal Coaching.

There is a growing consensus that traditional pre-service programs have not adequately prepared candidates for the principalship. National principals’ organizations and new legislation call for induction programs for novice principals that include mentoring. It is clear that experienced principals also need ongoing support and professional development, and that a coach or mentor can be a key element of this process (ERS, 2000).
How You Move Is What I See: Planning an Action Biases a Partner’s Visual Search

Activating action representations can modulate perceptual processing of action-relevant dimensions, indicative of a common-coding of perception and action. When two or more agents work together in joint action, individual agents often need to consider not only their own actions and their effects on the world, but also predict the actions of a co-acting partner. If in these situations the action of a partner is represented in a functionally equivalent way to the agent’s own actions, one may also expect interaction effects between action and perception across jointly acting individuals. The present study investigated whether the action of a co-acting partner may modulate an agent’s perception. The “performer” prepared a grasping or pointing movement toward a physical target while the “searcher” performed a visual search task. The performer’s planned action impaired the searcher’s perceptual performance when the search target dimension was relevant to the performer’s movement execution. These results demonstrate an action-induced modulation of perceptual processes across participants and indicate that agents represent their partner’s action by employing the same perceptual system they use to represent an own action. We suggest that task representations in joint action operate along multiple levels of a cross-brain predictive coding system, which provides agents with information about a partner’s actions when they coordinate to reach a common goal.
Prooxidants prevent yeast cell death induced by genotoxic stress

It was shown earlier that DNA damage induced by alkylating agent MMS (methyl methanesulfonate) results in formation of ROS (reactive oxygen species) in yeast cells. Here, we asked whether this ROS generation is favourable for the cells. It appeared that prooxidants rather than antioxidants stimulate the survival after MMS treatment. We found that positively charged detergents increase the survival via induction of H2O2 formation in the cells. Interestingly, prooxidants protected yeast cells from the moderate doses of MMS and enhanced the toxicity of relatively high ones. Prooxidants also protect the cells arrested in mitosis (nocodazole treatment), indicating that the protection is mostly due to ROS‐mediated transcriptional stress—response rather than due to enrichment of cell culture with highly MMS‐resistant G2/M cells. The comparison of the published expression profile responses to prooxidant and MMS treatments identifies a set of ROS‐activated genes, which are likely to protect cells from the genotoxic stress.
An Examination of the Nature of Reading Fluency

The present study attempted to investigate the underlying cognitive and linguistic skills necessary for three different aspects of reading fluency: rate, phrasing, quality of expression. The variance accounted for by each of these skills on measures of reading comprehension was also evaluated. Oral reading skills of thirdand fourth-grade normal readers were assessed on narrative passages within each participant's independent reading level (i.e., fewer than two percent word reading errors). Results indicated similarities in the cognitive and reading skills necessary for rapid reading and appropriate phrasing. Specifically, word recognition was the strongest predictor in both cases. However, oromotor accuracy and rapid serial naming also accounted for significant portions of variance in both reading rate and phrasing skill, after controlling for age and/or independent reading level. In addition, working memory was a significant predictor of reading rate. Linguistic measures of syntax knowledge and listening comprehension did not contribute significantly to variance in phrasing. The assessment tool created to evaluate quality of phrasing and expression is presented. Limitations of this study and suggestions for future research also are discussed.
A Novel Mutation in the Upstream Open Reading Frame of the CDKN1B Gene Causes a MEN4 Phenotype

The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27KIP1, an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27KIP1 expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5′UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF–encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27KIP1 expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27KIP1 activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27KIP1 activity can also be modulated by an uORF and mutations affecting uORF could change p27KIP1 expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases.
Estimating Forest Ecosystem Evapotranspiration at Multiple Temporal Scales With a Dimension Analysis Approach 1

Abstract: It is critical that evapotranspiration (ET) be quantified accurately so that scientists can evaluate the effects of land management and global change on water availability, streamflow, nutrient and sediment loading, and ecosystem productivity in watersheds. The objective of this study was to derive a new semi‐empirical ET modeled using a dimension analysis method that could be used to estimate forest ET effectively at multiple temporal scales. The model developed describes ET as a function of water availability for evaporation and transpiration, potential ET demand, air humidity, and land surface characteristics. The model was tested with long‐term hydrometeorological data from five research sites with distinct forest hydrology in the United States and China. Averaged simulation error for daily ET was within 0.5 mm/day. The annual ET at each of the five study sites were within 7% of measured values. Results suggest that the model can accurately capture the temporal dynamics of ET in forest ecosystems at daily, monthly, and annual scales. The model is climate‐driven and is sensitive to topography and vegetation characteristics and thus has potential to be used to examine the compounding hydrologic responses to land cover and climate changes at multiple temporal scales.
Reconstructing curves in three (and higher) dimensional space from noisy data

We consider the task of reconstructing a curve in constant dimensional space from noisy data. We consider curves of the form <i>C = [(x,y<sub>1</sub>,•••,y<sub>c</sub>) | y<sub>j</sub> = p<sub>j</sub>(x)]</i>, where the <i>p<sub>j</sub></i>'s are polynomials of low degree. Given <i>n</i> points in <i>(c+1)</i>-dimensional space, such that <i>t</i> of these lie on some such unknown curve <i>C</i> while the other <i>n-t</i> are chosen <i>randomly and independently</i>, we give an efficient algorithm to recover the curve <i>C</i> and the identity of the good points. The success of our algorithm depends on the relation between <i>n</i>, <i>t</i>, <i>c</i> and the degree of the curve <i>C</i>, requiring <i>t = Ω (n deg(C)) <sup>1/(c+1)</sup></i>. This generalizes, in the restricted setting of random errors, the work of Sudan (J. Complexity, 1997) and of Guruswami and Sudan (IEEE Trans. Inf. Th. 1999) that considered the case <i>c=1</i>.
Reconstructing grasping motions from high-frequency local field potentials in primary motor cortex

Recent developments in neural interface systems hold the promise to restore movement in people with paralysis. In search of neural signals for control of neural interface systems, previous studies have investigated primarily single and multiunit activity, as well as low frequency local field potentials (LFPs). In this paper, we investigate the information content about grasping motion of a broad band high frequency LFP (200 Hz – 400 Hz) by classifying discrete grasp aperture states and decoding continuous aperture trajectories. LFPs were recorded via 96-microelectrode arrays in the primary motor cortex (M1) of two monkeys performing free 3-D reaching and grasping towards moving objects. Our results indicate that broad band high frequency LFPs could serve as useful signals for restoring a motor function such as grasp control.
Team Association Analysis for Named Entity Filtering

Abstract : This paper describes the participation of the Universities of Helsinki and Caen in the first round of the TREC Knowledge Base Acceleration track3. The task focused on filtering a stream of documents relevant to a set of entities. Our approach uses word co-occurrence graphs for modelling the named entities. We submitted two runs that achieved an average F-measure superior to the mean of all submitted runs. The best of those runs ranked in the top 5 runs for both the central and relevant F-measures, out of a total of 43 runs submitted by 11 institutions. As our runs were the produce of a first implementation of our approach these preliminary results are very supportive of our idea to use concept graphs for modelling named entity relations.
Exact air charge feed forward control of a turbocharged SI engine

In this work, a MIMO feed forward control for the air charge, i.e. the mass of air in the cylinders of a turbo charged spark ignition (SI) engine is presented. The control inputs are the angle of the throttle plate and the opening of the wastegate. There are many publications in this field of application. Often the control task is separated into an air charge control with the throttle plate as control input and a boost pressure control with the wastegate opening as control input. These approaches often lack the ability to precisely track reference trajectories in the transition between suction mode operation and turbocharged operation. The approach presented here is based on exact input-output linearization and enables a perfect tracking of air charge reference trajectories in both modes of operation and the transition between them.
Category‐specificity in the human medial temporal lobe cortex

The medial temporal lobe cortex (MTLC) occupies a pivotal position at the interface between neocortical association areas and the hippocampus. It has been suggested that the MTLC contains functionally distinct regions, with perirhinal cortex (PRc) preferentially supporting object processing and posterior parahippocampal cortex (PHc) preferentially supporting encoding of spatial information. Measuring differential BOLD responsiveness to objects, scenes, and other stimulus categories, we find a double dissociation between an anterior PRc response to objects and a posterior PHc response to scene stimuli. Furthermore, an anatomical ROI based approach was undertaken in an effort to understand the response profile underlying this double dissociation. We did not see any evidence for a sharp border between putatively distinct scene‐preferential and object‐preferential MTLC regions. Instead, scene‐preferential responsiveness was noted to drop off in a graded, linear fashion in successively anterior MTLC regions until object‐preferential responsiveness emerged in anterior PRc, although objects produced above baseline responses across the anterior–posterior extent of the parahippocampal gyrus. Other stimulus categories, such as faces and words, led to above baseline activation in either a few confined regions (faces) or none at all (words). Thus, what differentiated regions along the parahippocampal gryus was the relative response to objects and scenes, not simply above baseline responses to either category. This pattern raises the possibility that posterior PHc, and anterior PRc are situated at the ends of a single organizational continuum supported by the entire length of MTLC. © 2008 Wiley‐Liss, Inc.
Effect of insulating barriers in arc flash testing

Low voltage arc flash testing has been conducted using the standard IEEE1584 test procedure, but with the electrode tips terminated in an insulating barrier instead of in the open air. The barrier prevents downwards arc motion, has a stabilizing effect on the arcs, and produces a strong horizontal plasma cloud flow. It also produces shorter arc lengths, higher arcing currents and higher maximum incident energy density, when compared with the standard arrangement. Erosion of the copper electrodes is very high and this causes a much larger quantity of copper spray to be directed towards the outside of the box. Similar results can be observed when vertical conductors are terminated in real industrial components. The effect of the barrier and the source X/R on arc sustainability at 208V has also been studied. The barrier test arrangement is believed to be more representative of real-world equipment. It is proposed that an arrangement like this should be incorporated into future revisions of the IEEE 1584 testing standard.
Simulation framework for barrier lowering in Schottky barrier MOSFETs

In this paper we present a simulation framework to account for the Schottky barrier lowering models in SB-MOSFETs within the Synopsys TCAD Sentaurus tool-chain. The improved Schottky barrier lowering model for field emission is considered. A strategy to extract the different current components and thus predict accurately the on- and off-current regions are adressed.
Ontology-based web annotation framework for hyperlink structures

Heterogeneous and autonomous web sites contain information that cannot be easily processed by automated tools.To address the heterogeneity issues, one attempt is to addmetadata to Web pages to provide semantic description ofthe web pages and other kinds of web objects. This isalso known as web annotation. Ontology-based Web annotation (OWA) is a kind of web annotation that associatesontologies with annotations. Since each ontology is usually adopted by some user community, OWA therefore facilitates sharing of knowledge among users sharing the ontology. In our survey, we noted that most existing OWA approaches only annotate web pages, but not the hyperlinksamong them. This restricts the association of useful semantics to the hyperlinks between web pages. In this paper, wetherefore propose to annotate hyperlink information as partof OWA. Users can create annotations for hyperlink structures and to utilize such annotations in browsing links between web pages and querying web sites. We first presenta general OWA framework consisting different components.An XML-based annotation scheme for annotating hyperlinkstructures is also proposed.