Miracle-dz/UniFAR-FTUs huggingface dataset:
Intramitotic controls in the fission yeast Schizosaccharomyces pombe: the effect of cell size on spindle length and the timing of mitotic events

We have used a new cinemicroscopy technique in combination with antitubulin immunofluorescence microscopy to investigate the timing of mitotic events in cells of the fission yeast Schizosaccharomyces pombe having lengths at division between 7 and 60 microns. Wild-type fission yeast cells divide at a length of 14 microns. Separation of daughter nuclei (anaphase B) proceeds at a rate of 1.6 +/- 0.2 microns min-1, until the spindle extends the length of the cell. Coincident with spindle depolymerization, the nuclei reverse direction and take up positions that will become the center of the two daughter cells. This post-mitotic nuclear migration occurs at a rate of 1.4 +/- 0.5 microns- 1. In cells in which the weel+ gene is overexpressed fivefold and that have an average length at mitosis of 28 microns, the rate of nuclear separation was only slightly reduced but, as spindles in these cells measure 20-22 microns, the duration of anaphase B was extended by approximately 40%. By contrast, in the mutant weel.50, which divides at 7 microns, both the rate and duration of anaphase B were indistinguishable from wild type. Nuclei reach the ends of these cells earlier but remain there until a point corresponding to the time of postmitotic nuclear migration in wild type. Thus, the events of mitosis can be extended but not abbreviated. These results are discussed in terms of a mitotic termination control that monitors many different events, one of which is spindle elongation.
Immune complexes in serum and cerebrospinal fluid of multiple sclerosis patients and patients with other neurological diseases

Paired serum and cerebrospinal fluid (CSF) specimens from 30 multiple sclerosis (MS) patients and 30 patients with other neurological diseases (ONDs) were analyzed for the presence of immune complexes (ICs). With each of the 4 tests used, ICs were found more frequently in sera from both MS and OND patients than in sera from healthy blood donors. IC‐positivity for MS and OND patient CSF varied from 10‐33 % and from 10‐17 % in different tests. The number of IC‐positive sera or CSF in MS patients did not differ significantly from those in OND patients. For both MS and OND patients, the positivity pattern for serum and CSF specimens in each IC test was essentially unique. Furthermore, because several CSF IC‐positive and serum IC‐negative paired specimens were found, intrathecal IC formation may be independent of IC formation in peripheral blood. The presence of ICs in serum or CSF did not correlate with the clinical status of or laboratory data on the MS patients, nor was a correlation found with the diagnosis of the OND patients. In total, these results suggest that the presence or absence of ICs in MS or OND patients may simply reflect changes in the immunological regulation of individual patients.
Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator

Developments in genome‐wide association studies and the increasing availability of summary genetic association data have made application of Mendelian randomization relatively straightforward. However, obtaining reliable results from a Mendelian randomization investigation remains problematic, as the conventional inverse‐variance weighted method only gives consistent estimates if all of the genetic variants in the analysis are valid instrumental variables. We present a novel weighted median estimator for combining data on multiple genetic variants into a single causal estimate. This estimator is consistent even when up to 50% of the information comes from invalid instrumental variables. In a simulation analysis, it is shown to have better finite‐sample Type 1 error rates than the inverse‐variance weighted method, and is complementary to the recently proposed MR‐Egger (Mendelian randomization‐Egger) regression method. In analyses of the causal effects of low‐density lipoprotein cholesterol and high‐density lipoprotein cholesterol on coronary artery disease risk, the inverse‐variance weighted method suggests a causal effect of both lipid fractions, whereas the weighted median and MR‐Egger regression methods suggest a null effect of high‐density lipoprotein cholesterol that corresponds with the experimental evidence. Both median‐based and MR‐Egger regression methods should be considered as sensitivity analyses for Mendelian randomization investigations with multiple genetic variants.
Bio-inspired crawling locomotion of a multi-arm octopus-like continuum system

This paper presents a control algorithm to achieve crawling locomotion for a multi-arm robotic system inspired by live octopuses. First the paper introduces a dynamic model of a continuum arm. The model accounts for the key features relevant to crawling locomotion, namely longitudinal muscles and suckers that provide force interaction with the surrounding environment. This single arm model is then validated against live octopus data and expanded to an 8-arm system. Appropriate coordination algorithms of the eight arms result in crawling locomotion. The results of this work can be used to study the motor control schemes for both multiple continuum arm robots and live octopuses.
Distribution Fields

Optical flow, tracking, background subtraction, stereovision, alignment, registration have in common that they try to find correspondences between parts of the images. These correspondences are often computed by mapping the images to descriptors and comparing these. A good descriptor that enables robust matching will be therefore useful for all of these lowlevel problems. Some of the properties that such descriptor should have are: robustness (to image noise, small misalignments), smoothness to degradations (to spatial location, scale, brightness), smoothness in its representation and ability to adapt to different images easily. Having a common representation for multiple problems allows the combination of different problems to help constrain the solution better. Many examples of recent work leverage the combination of tracking and optical flow [4], tracking and background subtraction [22, 21] or segmentation and optical flow [20]. In this document we introduce distribution fields (DFs) as an image descriptor for lowlevel vision problems. We argue that many current image descriptors (i.e.: SIFT, HOG, kernel-based descriptors, geometric blur etc.) can be explained in terms of a DF, which is a distribution at each pixel over the feature space. This way different descriptors can be compared and combined. Many of these descriptors have some of the important properties described above. However, to our knowledge, only DF together with a set of operations associated to them can capture all of them. The rest of this document is organized as follows. In section 2 we explain the relationship between DFs and other descriptors. In section 3 we describe DFs, the operations over them and the meaning of these operations. In section 4 we present experiments comparing the basin of attraction of DFs and other descriptors’. In section 5 we apply DFs to object tracking and show state-of-the-art results.
A Survey of High-Level Parallel Programming Models

Increasingly heterogeneous and hierarchical parallel architectures are now mainstream, however, most of the traditional programming models are lowlevel and explicit, limiting portability, scalability, and productivity. Moreover, performance of applications that overspecify evaluation degree and order will suer as they fail to adapt to changing architectures. This paper surveys the properties, advantages, and disadvantages of highlevel approaches to parallel programming that are deemed more exible for eciently utilising modern and future heterogeneous architectures. First, we introduce the challenges that arise from recent architectural trends and continue by surveying and characterising the high-level approaches to parallel programming. Subsequently, we review parallelism management policies and mechanisms to control them by comparing several representative implementations, focussing on heterogeneous hardware. Thereafter, we briey illustrate the high-level approach based on recent case studies. Finally, we conclude by summarising our ndings and views on what we believe are most suitable programming models to eciently harness heterogeneous architectures without reducing productivity.
A computational formalization for partial evaluation

We formalize a partial evaluator for Eugenio Moggi's computational metalanguage. This formalization gives an evaluation-order independent view of binding-time analysis and program specialization, including a proper treatment of call unfolding. It also enables us to express the essence of ‘control-based binding-time improvements’ for let expressions. Specifically, we prove that the binding-time improvements given by ‘continuation-based specialization’ can be expressed in the metalanguage via monadic laws.
Shoogle: excitatory multimodal interaction on mobile devices

Shoogle is a novel, intuitive interface for sensing data withina mobile device, such as presence and properties of textmessages or remaining resources. It is based around activeexploration: devices are shaken, revealing the contents rattlingaround "inside". Vibrotactile display and realistic impactsonification create a compelling system. Inertial sensingis used for completely eyes-free, single-handed interactionthat is entirely natural. Prototypes are described runningboth on a PDA and on a mobile phone with a wireless sensorpack. Scenarios of use are explored where active sensing ismore appropriate than the dominant alert paradigm.
Development of Violence Across the Lifespan: A Preliminary Model

Violence has serious implications for both the victim and the wider community. The current adult rehabilitation programmes accept violent offenders ranged from 20 years and older. This age range could have serious rehabilitation consequences, as a twenty year olds violence and violence related goals may differ substantially to a 70 year old. For this reason an understanding of the development of violence and violence related goals can aide rehabilitation and punitive policies. A review of recent research highlights there are many methodological and empirical gaps in the development of violence whereby the current research aimed to assuage this issue. The current research used grounded theory to develop a model on the development of violence over the life-course. For this research twelve men currently incarcerated at Rimutaka Prison in a violence rehabilitation unit were interviewed. This method developed two models. The “Influences on violence development” model outlines how environment and personal choices had an impact on the development of violence. The “development of violence” model outlines the increasing severity and frequency of violence over time, and the increasing complexity of violence related goals. This model is nested within the influences on violence development model. Comparing the current models to Loeber et al‟s (1993) pathways model, and Sampson and Laub‟s life-course perspective on offending, has found support for both models. Thus this model‟s theoretical value lies within its ability to draw together other areas of research and provide a holistic understanding of both how and why violence develops. One implication of these models is the understanding of the varying influences of environment on violence, upon both different individuals and different ages. This implies that rehabilitation should perhaps follow a more individual based focus. There are many limitations to the research, the most salient one being lack of saturation in the model and low sample size.
Bridge deep learning to the physical world: An efficient method to quantize network

As better performance is achieved by deep convolutional network with more and more layers, the increasing number of weighting and bias parameters makes it only possible to be implemented on servers in cyber space but infeasible to be deployed in physical-world embedded systems because of huge storage and memory bandwidth requirements. In this paper, we proposed an efficient method to quantize the model parameters. Instead of taking the quantization process as a negative effect on precision, we regarded it as a regularize problem to prevent overfitting, and a two-stage quantization technique including soft- and hard-quantization is developed. With the help of our quantization method, not only 93.75% of the parameter memory size can be reduced by replacing the word length from 32-bit to 2-bit, but the testing accuracy after quantization is also better than previous approaches in some dataset, and the additional training overhead is only 3% of the ordinary one.
Physical Layer Network Coding Schemes over Finite and Infinite Fields

Direct application of network coding at the physical layer - physical layer network coding (PNC) - is a promising technique for two-way relay wireless networks. In a two-way relay network, relay nodes are used to relay two-way information flows between pairs of end nodes. This paper proposes a precise definition for PNC. Specifically, in PNC, a relay node does not decode the source information from the two ends separately, but rather directly maps the combined signals received simultaneously to a signal to be relayed. Based on this definition, PNC can be further sub-classed into two categories - PNCF (PNC over finite field) and PNCI (PNC over infinite field) - according to whether the network-code field (or groups, rings) adopted is finite or infinite. For each of PNCF and PNCI, we consider two specific estimation techniques for dealing with noise in the mapping process. The performance of the four schemes is investigated by means of analysis and simulation, assuming symbol-level time synchronization only.
A novel role for phagocytosis-like uptake in herpes simplex virus entry

It is becoming increasingly clear that herpesviruses can exploit the endocytic pathway to infect cells, yet several important features of this process remain poorly defined. Using herpes simplex virus-1 (HSV-1) as a model, we demonstrate that endocytosis of the virions mimic many features of phagocytosis. During entry, HSV-1 virions associated with plasma membrane protrusions followed by a phagocytosis-like uptake involving rearrangement of actin cytoskeleton and trafficking of the virions in large phagosome-like vesicles. RhoA GTPase was activated during this process and the mode of entry was cell type–specific. Clathrin-coated vesicles had no detectable role in virion trafficking as Eps15 dominant-negative mutants failed to affect HSV-1 uptake. Binding and fusion of the virion envelope with the phagosomal membrane is likely facilitated by clustering of nectin-1 (or HVEM) in phagosomes, which was observed in infected cells. Collectively, our data suggests a novel mode of uptake by which the virus can infect both professional and nonprofessional phagocytes.
Nucleo‐cytoplasmic cycling of the vitamin D receptor in the enterocyte‐like cell line, Caco‐2

We examined the effects of 1,25 dihydroxyvitamin D3 (1,25(OH)2D3) on the distribution and mobility of the vitamin D receptor (VDR) in the enterocyte‐like Caco‐2 cell. Confocal microscopy showed that a green fluorescent protein‐vitamin D receptor (GFP‐VDR) fusion protein is predominantly nuclear (58%) and it does not associate with the apical or basolateral membrane of proliferating or polarized, differentiated cells. In contrast to the previously studied cell types, neither endogenous VDR nor GFP‐VDR levels accumulate in the nucleus following 1,25(OH)2D3 treatment (100 nM, 30 min). However, in nuclear photobleaching experiments nuclear GFP‐VDR import was significantly increased by 1,25(OH)2D3 during both an early (0–5 min) and later (30–35 min) period (20% per 5 min). Compared to the natural ligand, nuclear import of GFP‐VDR was 60% lower in cells treated with the 1,25(OH)2D3 analog, 1‐alpha‐fluoro‐16‐ene‐20‐epi‐23‐ene‐26,27‐bishomo‐25‐hydroxyvitamin D3 (Ro‐26‐9228, 5 min, 100 nM). Downstream events like ligand‐induced association of VDR with chromatin at 1 h and the accumulation of CYP24 mRNA were significantly lower in Ro‐26‐9228 treated cells compared to 1,25(OH)2D3 (60 and 95% lower, respectively). Collectively our data are consistent with a role for ligand‐induced nuclear VDR import in receptor activation. In addition, ligand‐dependent VDR nuclear import appears to be balanced by export, thus accounting for the lack of nuclear VDR accumulation even when VDR import is significantly elevated. J. Cell. Biochem. 100: 617–628, 2007. © 2006 Wiley‐Liss, Inc.
Computational Genome-Wide Discovery of Aberrant Splice Variations with Exon Expression Profiles

Alternative splicing plays a prominent role in eukaryotic gene regulations that allow a single gene to generate the multiple mRNA products. The recent advent of GeneChipreg Human Exon 1.0 ST Array enables us to measure the exon expression profiles of human cells on a genome-wide scale. With this advent, analysis of functional gene regulation could be extended to detect not only differentially expressed genes, but also specific splicing events that occur in target cells, but not in normal controls. We address some statistical issues for the identification of biomarker splice variations with exon expression data. The proposed method involves the following steps: (1) Whole transcript analysis with the nonparametric analysis of variance (ANOVA) to identify potential biomarkers that present specific splice variations. (2) Meta-analysis for discriminating non-specific splice variations that are caused by clinical heterogeneity in the collected samples. In the analysis of human cells, controlling non-specific splicing factors is essential for success in the detection of biomarker splice variations because splice patterns are possibly affected by inter-individual differences in the collected samples. We demonstrate its utility and perform a whole transcript analysis of exon expression profiles of colorectal carcinoma.
Software Projects in an Academic Environment

The "software hut" is a course project that is used in conjunction with a graduate-level course in software engineering. The purpose of this project is to give the students some "real world" experience with the design and implementation of software. This paper describes the author's experience in using such a project and presents some suggestions on how a project should be organized.
Weakly Supervised Classification of Tweets for Disaster Management

Social media has quickly established itself as an important means that people, NGOs and governments use to spread information during natural or man-made disasters, mass emergencies and crisis situations. Given this important role, real-time analysis of social media contents to locate, organize and use valuable information for disaster management is crucial. In this paper, we propose self-learning algorithms that, with minimal supervision, construct a simple bag-of-words model of information expressed in the news about various natural disasters. Such a model is human-understandable, human-modifiable and usable in a realtime scenario. Since tweets are a diffferent category of documents than news, we next propose a model transfer algorithm, which essentially refines the model learned from news by analyzing a large unlabeled corpus of tweets. We show empirically that model transfer improves the predictive accuracy of the model. We demonstrate empirically that our model learning algorithm is better than several state of the art semi-supervised learning algorithms.
Intelligent learning environments for programming: The case for integration and adaptation

The area of intelligent tutoring systems for programming is one of the most well-investigated topics in the AI-Ed literature. A number of powerful techniques to help novice learners have been suggested, developed, and described in hundreds of papers . However the "real world" situation with classroom applications of these systems is no better than it was 20 years ago. We claim that more attention should be paid to the problem of integrating existing techniques and tools into more versatile learning environments . In this paper we discuss the problems of integrated intelligent learning environments (ILE) for programming and review existing research that forms the background for future research in this area. In particular, we will review our work on a student model-centered architecture for ILE.
Genome Sequence of Rhizobacterium Serratia marcescens Strain 90-166, Which Triggers Induced Systemic Resistance and Plant Growth Promotion

ABSTRACT The rhizobacterium Serratia marcescens strain 90-166 elicits induced systemic resistance against plant pathogens and herbivores and promotes plant growth under greenhouse and field conditions. Strain 90-166 secretes volatile compounds, siderophores, salicylic acid, and quorum-sensing autoinducers as bacterial determinants toward plant health. Herein, we present its draft genome sequence.
Estimating energy expenditure of animals using the accelerometry technique: activity, inactivity and comparison with the heart-rate technique

SUMMARY Several methods have been used to estimate the energy expenditure of free-ranging animals. A relatively new technique uses measures of dynamic body acceleration as a calibrated proxy for energy expenditure and has proved an excellent predictor of energy expenditure in active animals. However, some animals can spend much of their time inactive and still expend energy at varying rates for a range of physiological processes. We tested the utility of dynamic body acceleration to estimate energy expenditure during a range of active (locomotion, eating) and inactive (digesting, thermoregulating) behaviours exhibited by domestic chickens. We also compared this technique with the more established heart-rate method for estimating energy expenditure. During activity, the error of estimation using body acceleration was very similar to that from the heart-rate method. Importantly, our results also showed that body acceleration can be used to estimate energy expenditure when birds are inactive. While the errors surrounding these estimates were greater than those during activity, and those made using the heart-rate method, they were less than those made using interspecific allometric equations. We highlight the importance of selecting a methodology that is appropriate for the life-history of the subject animal. We suggest that, to achieve the greatest possible accuracy and precision when estimating energy expenditure in free-ranging animals, the two techniques should be combined, and both heart rate (fH) and dynamic body acceleration could be included as covariates in predictive models. Alternatively, measures of acceleration can be used to ascertain which behaviour is being exhibited at each moment and hence which predictive model should be applied.
Guidelines on the use of Fit tables in software maintenance tasks: Lessons learned from 8 experiments

Executable acceptance test case-in particular Fit (Framework for Integrated Test) tables-originally intended for the development phase proved useful in maintenance activities too. Empirical evidence suggests that Fit tables are useful in improving the comprehension of change requirements and the correctness of the maintained code. Stemming from eight experiments formerly performed by the authors, this paper presents a set of lessons learned and guidelines useful for project managers on the use of Fit tables in maintenance tasks. Specifically, the paper discusses the use of Fit tables in maintenance tasks considering a set of dimensions, ranging from maintainerspsila experience to the nature of application being maintained and to the kind of benefits introduced by Fit tables. Benefits of Fit tables, such as improving the code correctness and comprehension, increase with developers experience and complex requirements but decrease with Web-based applications and when programmers work in pairs.