Miracle-dz/UniFAR-FTUs huggingface dataset:
Lgl2 Executes Its Function as a Tumor Suppressor by Regulating ErbB Signaling in the Zebrafish Epidermis

Changes in tissue homeostasis, acquisition of invasive cell characteristics, and tumor formation can often be linked to the loss of epithelial cell polarity. In carcinogenesis, the grade of neoplasia correlates with impaired cell polarity. In Drosophila, lethal giant larvae (lgl), discs large (dlg), and scribble, which are components of the epithelial apico-basal cell polarity machinery, act as tumor suppressors, and orthologs of this evolutionary conserved pathway are lost in human carcinoma with high frequency. However, a mechanistic link between neoplasia and vertebrate orthologs of these tumor-suppressor genes remains to be fully explored at the organismal level. Here, we show that the pen/lgl2 mutant phenotype shares two key cellular and molecular features of mammalian malignancy: cell autonomous epidermal neoplasia and epithelial-to-mesenchymal-transition (EMT) of basal epidermal cells including the differential expression of several regulators of EMT. Further, we found that epidermal neoplasia and EMT in pen/lgl2 mutant epidermal cells is promoted by ErbB signalling, a pathway of high significance in human carcinomas. Intriguingly, EMT in the pen/lgl2 mutant is facilitated specifically by ErbB2 mediated E-cadherin mislocalization and not via canonical snail–dependent down-regulation of E-cadherin expression. Our data reveal that pen/lgl2 functions as a tumor suppressor gene in vertebrates, establishing zebrafish pen/lgl2 mutants as a valuable cancer model.
ATP Crossing the Cell Plasma Membrane Generates an Ionic Current in Xenopus Oocytes*

The presence of ATP within cells is well established. However, ATP also operates as an intercellular signal via specific purinoceptors. Furthermore, nonsecretory cells can release ATP under certain experimental conditions. To measure ATP release and membrane currents from a single cell simultaneously, we usedXenopus oocytes. We simultaneously recorded membrane currents and luminescence. Here, we show that ATP release can be triggered in Xenopus oocytes by hyperpolarizing pulses. ATP release (3.2 ± 0.3 pmol/oocyte) generated a slow inward current (2.3 ± 0.1 μA). During hyperpolarizing pulses, the permeability for ATP4– was more than 4000 times higher than that for Cl–. The sensitivity to GdCl3 (0.2 mm) of hyperpolarization-induced ionic current, ATP release and E-ATPase activity suggests their dependence on stretch-activated ion channels. The pharmacological profile of the current inhibition coincides with the inhibition of ecto-ATPase activity. This enzyme is highly conserved among species, and in humans, it has been cloned and characterized as CD39. The translation, in Xenopus oocytes, of human CD39 mRNA encoding enhances the ATP-supported current, indicating that CD39 is directly or indirectly responsible for the electrodiffusion of ATP.
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches

SUMMARY We have developed a tool, called ProbeMatch, for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike most of the existing tools such as ELAND which only perform ungapped alignments allowing at most two mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to three errors including insertion, deletion and mismatch. To speedup sequence alignment, ProbeMatch uses gapped q-grams and q-grams of various patterns to identify target hits to a query sequence. This approach results in fewer initial sequences to examine with no loss in sensitivity. ProbeMatch has been used to align 169,095 Illumina GAII reads against the human genome, which could not be mapped by ELAND, and found alignments for 28,625 reads of the 169,095 reads in less than 3 h. AVAILABILITY Source code is freely available at (http://www.cs.wisc.edu/~jignesh/probematch/).
Anisotropic vector diffusion in image smoothing

Anisotropic diffusion has been widely used in image processing for its efficiency of smoothing the noisy images while preserving the sharp edges. In this paper we explore a general version of anisotropic diffusion schemes for vector-valued images, based on the polar-coordinate representation of the vectors. As an example, we apply our method to color images and show its ability of edge-preserving smoothing on vector-valued images.
Harnessing paradata and multilevel multiple imputation when analysing survey data: a case study

Abstract Missing data (attrition and non-response) are a feature of most surveys especially longitudinal/panel studies. And many such studies now have multilevel designs and hence multilevel data structures. Recent advances in imputation methodology now offer social researchers opportunities to address issues of missing data in a statistically principled way. Paradata can offer great insights in understanding the nature and causes of missingness and can be used to construct auxiliary variables to be included in imputation models. In this paper we present multilevel multiple imputation which has recently extended MI to incorporate multilevel data, making it a flexible and robust strategy for many research settings. We illustrate the procedures by analysing data drawn from a longitudinal study of prisoners. We show how paradata of that study was instrumental in guiding our approach and subsequent analysis.
Discovering Learning Antecedents in Learning Analytics Literature

We investigated various learning antecedents that have been the research subjects of Learning Analytics (LA) studies and explored the content and quantity of the LA literature with respect to each antecedent through text mining the LAK dataset. Our goal was to simultaneously reveal to what extent do LA researchers address learning antecedents and how they incorporated these in the implementation of LA solutions (e.g. models and software technologies) to facilitate and augment student learning. Instead of taking a pure text mining approach, we undertook a slightly different strategy by (i) identifying antecedents of student learning by examining extant literature on learning and educational theories and (ii) identifying which among the theoretically relevant antecedents are currently reported in LA studies. The analytical techniques we employed were a mix of domain-based analysis and corpus analytics which included association analysis and keyphrase extraction. The results showed that most LA studies are geared toward capturing and measuring student awareness and promoting social learning and less on goal-setting and self-efficacy. Through this work we hope to encourage the LA community to dedicate research efforts to also investigate other relatively neglected yet promising learning antecedents.
HiPE on AMD64

Erlang is a concurrent functional language designed for developing large-scale, distributed, fault-tolerant systems. The primary implementation of the language is the Erlang/OTP system from Ericsson. Even though Erlang/OTP is by default based on a virtual machine interpreter, it nowadays also includes the HiPE (High Performance Erlang) native code compiler as a fully integrated component. This paper describes the recently developed port of HiPE to the AMD64 architecture. We discuss technical issues that had to be addressed when developing the port, decisions we took and why, and report on the speedups (compared with BEAM) which HiPE/AMD64 achieves across a range of Erlang programs and how these compare with speedups for the more mature SPARC and x86 back-ends.
International Comparisons of Alcohol Consumption

International comparisons of alcohol consumption and its consequences can serve multiple purposes. For example, despite differences among countries in drinking cultures, drink sizes and strengths, and methods of measuring alcohol consumption, international survey research has provided a substantial amount of information on the rates of abstinence or current drinking, the frequency of drinking or binge drinking, and the mean consumption among both adults and youths in many countries. Other studies using aggregate-level data have analyzed per capita alcohol consumption in various countries. These studies can be used to relate per capita consumption to certain alcohol-related outcomes and to evaluate changes of both consumption and different outcomes within a country or across countries over time. Some problems associated with international research, however, such as issues of comparability of surveys, still need to be resolved.
Learning variable length units for SMT between related languages via Byte Pair Encoding

We explore the use of segments learnt using Byte Pair Encoding (referred to as BPE units) as basic units for statistical machine translation between related languages and compare it with orthographic syllables, which are currently the best performing basic units for this translation task. BPE identifies the most frequent character sequences as basic units, while orthographic syllables are linguistically motivated pseudo-syllables. We show that BPE units modestly outperform orthographic syllables as units of translation, showing up to 11% increase in BLEU score. While orthographic syllables can be used only for languages whose writing systems use vowel representations, BPE is writing system independent and we show that BPE outperforms other units for non-vowel writing systems too. Our results are supported by extensive experimentation spanning multiple language families and writing systems.
Simultaneous Multikernel GPU: Multi-tasking throughput processors via fine-grained sharing

Studies show that non-graphics programs can be less optimized for the GPU hardware, leading to significant resource under-utilization. Sharing the GPU among multiple programs can effectively improve utilization, which is particularly attractive to systems where many applications require access to the GPU (e.g., cloud computing). However, current GPUs lack proper architecture features to support sharing. Initial attempts are preliminary: They either provide only static sharing, which requires recompilation or code transformation, or they do not effectively improve GPU resource utilization. We propose Simultaneous Multikernel (SMK), a fine-grain dynamic sharing mechanism, that fully utilizes resources within a streaming multiprocessor by exploiting heterogeneity of different kernels. We propose several resource allocation strategies to improve system throughput while maintaining fairness. Our evaluation shows that for shared workloads with complementary resource occupancy, SMK improves GPU throughput by 52% over non-shared execution and 17% over a state-of-the-art design.
Participation in Information Markets Research: A New Conceptualization and Measurement

Participation is a fundamental concept in information systems research. It has been viewed to be a promising factor for the success of any IT system. However, its complex nature with respect to its conceptualization and measurement reported mix findings to the literature. In this paper, a literature review is conducted across many research disciplines to find a solid ground for proposing definition and new measures for assessing computer-recorded (e.g. online) participation. Specifically, this paper redefines traditional views on IS-related participation into a new conceptualization, and proposes methods for its operationalization to appropriately fit within recent technological contexts such as information markets.
The Changes in the Circulation After Birth: Their Importance in Congenital Heart Disease

Circulatory changes at birth have a profound influence on the physiology of the circulation in normal infants and those with congenital heart disease. Since the concept that cardiac defects are fixed entities is being superseded by an appreciation of the changing nature of physiologic disturbances and their clinical consequence, the course and distribution of the fetal circulation with the influences of the major changes at birth, including changes in pulmonary vascular resistance, and closure of the ductus arteriosus and foramen ovale, require study. This lecture traces these and other changes and discusses their influences on congenital heart disease.
Mechanisms Underlying the Prosocial Construction Effect: Detail and Self-referential Processing

There is growing interest in the links between memory and imagination and in their contributions to other cognitive functions. In previous research, imagining oneself helping others increased one’s willingness to help them, and willingness to help correlated with the subjective vividness of imagination (i.e., the prosocial construction effect; PCE). We investigated the degree to which the PCE relies on self-referential processing and on more objectively measured vividness, and the relationship between episodic memory and self-reported trait empathy. We conclude that 1) self-reference is an important but not a necessary component of the PCE; 2) its role may relate to increased feelings of compassion; 3) the PCE is not limited to subjective vividness but can be demonstrated using more objective measures of vividness; and 4) self-reported trait empathy is higher when survey items cue memories of one’s own empathetic behaviour. Implications and avenues for future research are discussed.
Small unmanned aerial vehicles (micro-UAVs, drones) in plant ecology

Premise of the study: Low-elevation surveys with small aerial drones (micro–unmanned aerial vehicles [UAVs]) may be used for a wide variety of applications in plant ecology, including mapping vegetation over small- to medium-sized regions. We provide an overview of methods and procedures for conducting surveys and illustrate some of these applications. Methods: Aerial images were obtained by flying a small drone along transects over the area of interest. Images were used to create a composite image (orthomosaic) and a digital surface model (DSM). Vegetation classification was conducted manually and using an automated routine. Coverage of an individual species was estimated from aerial images. Results: We created a vegetation map for the entire region from the orthomosaic and DSM, and mapped the density of one species. Comparison of our manual and automated habitat classification confirmed that our mapping methods were accurate. A species with high contrast to the background matrix allowed adequate estimate of its coverage. Discussion: The example surveys demonstrate that small aerial drones are capable of gathering large amounts of information on the distribution of vegetation and individual species with minimal impact to sensitive habitats. Low-elevation aerial surveys have potential for a wide range of applications in plant ecology.
International school students’ experiences of their local environment: a case study from Qatar

Interest in children’s experiences of their local environment is growing in education studies, geography and environmental psychology in response to increasing interests in children’s everyday lives and personal geographies. Within international education research, those studies exploring experiences of international school education tend to explore senses of belonging, identity and notions of ‘home’. However, the direct and embodied relationship expatriate children have with their local environment, and experiences of place, is a neglected field of study. The geographical context of this research in a gated compound in Qatar is significant. A growing volume of research from a variety of disciplines, notably urban planning studies, cultural geography and anthropology, have started to explore gated communities as a feature of living spaces across the world – often for wealthy nationals and expatriates in countries with more extreme inequalities in wealth distribution. However, research focusing on the experiences of (expatriate) children learning and growing up in such contexts is limited. This research explores how children living in a gated expatriate enclave in Qatar experience their local environment. With the rise in the number of gated communities and the growth of expatriate enclaves globally, this is a significant area of research with potential implications for educators and communities beyond the case study area. The findings of this research suggest that boundedness and surveillance in the gated community impact interactions with and constructions of space and place, limiting free exploration of the wider environment and, host country interaction, and creating binary constructions of insides/outsides and insiders/outsiders. The research suggests ways in which educators in similar contexts can adapt and adopt geographical theory such as ‘critical thirding’ to help children deconstruct physical, social and imagined boundaries in their local environment, and critically engage with and participate in place-making in their local area. Furthermore, the potential for the incorporation of place-based educational practices is examined.
Reverse-engineering of UML 2.0 Sequence Diagrams from Execution Traces

To fully understand the behavior of a program, it is crucial to have ef? cient techniques to reverse dynamic views of the program. In this paper, we focus on the reverse engineering of UML 2.0 sequence diagrams showing loops and alternatives from execution traces. To build these complete sequence diagrams, we need to capture the systems state through dynamic analysis. We propose to build state vectors through trace analysis and we precisely discuss how the state of an object-oriented system can be captured. We also present an adaptable trace analysis tool that we have developed to experiment the ideas presented in this work.
Time Course of Gene Expression Profiling in the Liver of Experimental Mice Infected with Echinococcus multilocularis

Background Alveolar echinococcosis (AE) is a severe chronic parasitic disease which behaves like a slow-growing liver cancer. Clinical observations suggest that the parasite, Echinococcus multilocularis (E. multilocularis) influences liver homeostasis and hepatic cell metabolism. However, this has never been analyzed during the time course of infection in the common model of secondary echinococcosis in experimental mice. Methodology/Principal Findings Gene expression profiles were assessed using DNA microarray analysis, 1, 2, 3 and 6 months after injection of E. multilocularis metacestode in the liver of susceptible mice. Data were collected at different time points to monitor the dynamic behavior of gene expression. 557 differentially expressed genes were identified at one or more time points, including 351 up-regulated and 228 down-regulated genes. Time-course analysis indicated, at the initial stage of E. multilocularis infection (month 1–2), that most of up-regulated pathways were related to immune processes and cell trafficking such as chemokine-, mitogen-activated protein kinase (MAPK) signaling, and down-regulated pathways were related to xenobiotic metabolism; at the middle stage (month 3), MAPK signaling pathway was maintained and peroxisome proliferator-activated receptor (PPAR) signaling pathway emerged; at the late stage (month 6), most of up-regulated pathways were related to PPAR signaling pathway, complement and coagulation cascades, while down-regulated pathways were related to metabolism of xenobiotics by cytochrome P450. Quantitative RT-PCR analysis of a random selection of 19 genes confirmed the reliability of the microarray data. Immunohistochemistry analysis showed that proliferating cell nuclear antigen (PCNA) was increased in the liver of E. multilocularis infected mice from 2 months to 6 months. Conclusions E. multilocularis metacestode definitely exerts a deep influence on liver homeostasis, by modifying a number of gene expression and metabolic pathways. It especially promotes hepatic cell proliferation, as evidenced by the increased PCNA constantly found in all the experimental time-points we studied and by an increased gene expression of key metabolic pathways.
Integer Matrix Factorization and Its Application

Matrix factorization has been of fundamental importance in modern sciences and technology. This work investigates the notion of factorization with entries restricted to integers or binaries, , where the “integer” could be either the regular ordinal integers or just some nominal labels. Being discrete in nature, such a factorization or approximation cannot be accomplished by conventional techniques. Built upon a basic scheme of rank one approximation, an approach that recursively splits (approximates) the underlying matrix into a sum of rank one matrices with discrete entries is proposed. Various computational issues involved in this kind of factorization, which must take into account the metric being used for measurement, are addressed. The mechanism presented in this paper can handle multiple types of data. For application purposes, the discussion emphasizes mainly on binaryinteger factorizations. But the notion is readily generalizable with slight modifications to, for example, integer-integer factorizations. Applications to cluster analysis and pattern discovery are demonstrated through some real-world data. Of particular interest is the result on the ordering of rank one approximations which, in a remote sense, is the analogy for discrete data to the ordering of singular values for continuous data. As such, a truncated low rank factorization (for discrete data) analogous to the truncated singular value decomposition is also obtained.
Reusing Previously Found A* Paths for Fast Goal-Directed Navigation in Dynamic Terrain

Generalized Adaptive A* (GAA*) is an incremental algorithm that replans using A* when solving goal-directed navigation problems in dynamic terrain. Immediately after each A* search, it runs an efficient procedure that updates the heuristic values of states that were just expanded by A*, making them more informed. Those updates allow GAA* to speed up subsequent A* searches. Being based on A*, it is simple to describe and communicate; however, it is outperformed by other incremental algorithms like the state-of-the-art D*Lite algorithm at goal-directed navigation. In this paper we show how GAA* can be modified to exploit more information from a previous search in addition to the updated heuristic function. Specifically, we show how GAA* can be modified to utilize the paths found by a previous A* search. Our algorithm — Multipath Generalized Adaptive A* (MPGAA*) — has the same theoretical properties of GAA* and differs from it by only a few lines of pseudocode. Arguably, MPGAA* is simpler to understand than D*Lite. We evaluate MPGAA* over various realistic dynamic terrain settings, and observed that it generally outperforms the state-of-the-art algorithm D*Lite in scenarios resembling outdoor and indoor navigation.
Global P, PP, and PKP wave microseisms observed from distant storms

Microseisms are the continuous background vibrations of the Earth observed between earthquakes. Most microseism studies have focused on low frequency energy (0.05–0.5 Hz) propagating as surface waves, but in the microseism spectrum there is also energy that propagates as body waves (P‐waves). Using array analysis on southern California stations we show that these body waves are generated in the ocean from distant storms and propagate deep within the Earth's mantle and core as P, PP and PKP phases. Comparisons with ocean wave hindcast data identify several distinct source regions in both the northern and southern hemispheres. Analyses of these body waves demonstrate that microseisms often have a strong P‐wave component originating from distant locations.