Miracle-dz/UniFAR-FTUs huggingface dataset:
Relocalization of DNA lesions to the nuclear pore complex

Abstract Early screens in yeast for mutations exhibiting sensitivity to DNA damage identified nuclear pore components, but their role in DNA repair was not well understood. Over the last decade, studies have revealed that several types of persistent DNA lesions relocate to either the nuclear pore complex (NPC) or nuclear envelope (NE). Of these two sites, the nuclear pore appears to be crucial for DNA repair of persistent double-strand breaks, eroded telomeres and sites of fork collapse at expanded CAG repeats. Using a combination of cell biological imaging techniques and yeast genetic assays for DNA repair, researchers have begun to understand both the how and why of lesion relocation to the NPC. Here we review the types of lesions that relocate to the NPC, mediators of relocation and the functional consequences of relocation understood to date. The emerging theme is that relocation to the NPC regulates recombination to influence repair pathway choice and provide a rescue mechanism for lesions or DNA structures that are resistant to repair.
Implementing As-Rigid-As-Possible Shape Manipulation and Surface Flattening

This article provides a description of an "as-rigid-as-possible shape manipulation" implementation that is clearer and easier to understand than the original. While the original paper used triangle-based representation, we use edgebased representation to simplify the coding. We also extend the original algorithm to allow the user to place handles on arbitrary positions of the mesh. In addition, we show that the same algorithm can be used for surface flattening with quality and performance comparable to popular flattening methods.
Random Fluctuations in Scaled MOS Devices

Today, variability is recognized as a major obstacle for continuing MOS transistor miniaturization. Among various kinds of variability, this paper mainly focuses on random fluctuation, which is caused by microscopic perturbations, such as discreteness of charges and atomic scale structural irregularity. Some recent research results for quantitatively understanding the causes of random fluctuation are reviewed. Methods of reducing random fluctuation will be discussed.
gHA: An Efficient and Iterative Checkpointing Mechanism for Virtualized GPUs

Graphic Process Unit (GPU) is the core for graphics computation. Because of its parallel nature it has potential to enhance the computation in a wide range. An example is the adoption of GPU virtualization in the cloud environment for high performance computing. However, GPU has its limitations. For various reasons GPU may hang in applications, whilst full GPU virtualization does not support live migration like CPU in Xen. The state-of-the-art method to get round is to reset the GPU hardware via a specific mechanism provided by GPU vendors. The disadvantage of such reset operation is that it causes application unavailability in order to maintain stability of the operating system. This paper presents an efficient method to address the above limitations. In particular, we start from the gVirt [28] method, and develop a novel checkpointing mechanism within our open source solution1 which we define as High Availability gVirt (gHA for short). The key of our scheme is to checkpoint and back up the whole Virtual Machine (VM) to a new host. In circumstances when GPU hangs, the backup VM takes over to guarantee the high availability of the virtualized environment. Not surprisingly, overhead occurs when our checkpointing mechanism is applied. Our tests show that downtime of the VM backup is between 220 ms and 400 ms, only 100-200 ms more than the idle VM without GPU virtualization support, which is a quite acceptable result. For numerous GPU workload tests, our evaluation shows that different GPU workloads achieve 65-92% of gVirt performance, which is a good trade-off between performance and stability. Our solution occupies 80-180Mbps bandwidth during execution, which is fairly manageable as the total bandwidth of 1Gbps between the two hosts.
Towards Automatic Extraction of Argument Structure from Corpora

The valency of predicates is a key component of a lexical entry because most, if not all, recent syntactic theories`project' syntactic structure from such information in the lexicon (e.g. Pollard & Sag, 1987). Therefore, a wide-coverage robust parser utilising a grammar based on one of these theories must have access to an accurate dictionary encoding (at a minimum) valency information and probably further details of argument structure. However, as designers of natural language processing systems have observed (e.g. Jensen, 1991) valency is closely associated to lexical sense and the senses of a word change between corpora, sublanguages and/or subject domains. Jensen et al (1994) take this as evidence that the coupling between syntactic parsing and valency information should be much weaker than in current syntactic theories. From a more theoretical standpoint, Grimshaw (1990), Pustejovsky (1993) and others have argued that valency should instead be projected from lexical semantic information. In a recent experiment with a wide-coverage parsing system utilising a grammatical framework based on standard lexicalist assumptions, Briscoe & Carroll (1993) observed that over half the analysis failures on unseen corpus examples were caused by incorrect subcategorisation for predicate valency. Because of the close connection between sense and valency and between subject domain and sense, it may be that a fully accuratèstatic' valency dictionary of the language is unattainable. The work we describe below could equally support a large-scale attempt to construct such a dictionary from substantial quantities of corpus material, or the less ambitious and more frequent construction of`disposable' dictionaries or augmentation of`self-updating' dictionaries as and when new corpora need to be parsed. We have developed a system which is potentially capable of delivering puta-tive lexical entries for predicates extracted from textual corpora, focussing on the acquisition ofàrgument structure' (deened as valency, semantic selectional restrictions/preferences, diathesis alternations, bounded dependency rules, such as passive or particle movement, and control of understood arguments in pred-icative complements) { though so far we have mostly explored predictions with respect to valency. The approach we have adopted is to construct a `shallow' syntactic but global analysis of sentences for corpus material annotated with part-of-speech and punctuation mark sequences disambiguated by a tagger. We then extract relevant competing subanalyses surrounding a given predicate from all possible shallow analyses of sentences. These so-called patternsets for a given predicate are then evaluated using heuristics and a simple probabilistic approximation of the correctness of a given pattern, so …
Design and architecture of a friend recommender system in the social bookmarking domain

Social media systems are becoming more and more popular nowadays. In order to face the overload in the amount of users and content available in these systems, social recommender systems have been developed and are largely studied in the literature. A form of social media, known as social bookmarking system, allows to share bookmarks in a social network. A user adds as a friend or follows another user and receives updates on the bookmarks added by that user. However, no approach in the literature proposes friend recommender systems in the social bookmarking domain. In this paper, we present an analysis of the state-of-the-art on user recommendation in social environments and of the structure of a social bookmarking system, in order to derive a design and an architecture of a friend recommender system in the social bookmarking domain. This study can be useful for any future research in this area, by highlighting the aspects that characterize this domain and the features that this type of recommender system has to offer.
Antiproliferative Effects of Methanolic Extracts of Cryptocarya concinna Hance Roots on Oral Cancer Ca9-22 and CAL 27 Cell Lines Involving Apoptosis, ROS Induction, and Mitochondrial Depolarization

Cryptocarya-derived natural products were reported to have several biological effects such as the antiproliferation of some cancers. The possible antioral cancer effect of Cryptocarya-derived substances was little addressed as yet. In this study, we firstly used the methanolic extracts of C. concinna Hance roots (MECCrt) to evaluate its potential function in antioral cancer bioactivity. We found that MECCrt significantly reduced cell viability of two oral cancer Ca9-22 and CAL 27 cell lines in dose-responsive manners (P < 0.01). The percentages of sub-G1 phase and annexin V-positive of MECCrt-treated Ca9-22 and CAL 27 cell lines significantly accumulated (P < 0.01) in a dose-responsive manner as evidenced by flow cytometry. These apoptotic effects were associated with the findings that intracellular ROS generation was induced in MECCrt-treated Ca9-22 and CAL 27 cell lines in dose-responsive and time-dependent manners (P < 0.01). In a dose-responsive manner, MECCrt also significantly reduced the mitochondrial membrane potential in these two cell lines (P < 0.01–0.05). In conclusion, we demonstrated that MECCrt may have antiproliferative potential against oral cancer cells involving apoptosis, ROS generation, and mitochondria membrane depolarization.
Admissible number of users in OFDM/TDMA based wireless systems through loss probability estimation considering multifractal traffic modeling

In this paper, we present an admission control scheme for an OFDM (Orthogonal Frequency-Division Multiplexing)/TDMA(Time Division Multiplexing Access) based wireless system taking into account the multifractal behaviour of the traffic flows. To this end, first, we show evidences of multifractal characteristics on wireless network traffic traces. These findings motivated us to derive a data loss probability expression that can be applied to the OFDM/TDMA based wireless system. Moreover, the loss probability expression is used to control the admission of new users to the OFDM/TDMA system. Simulations and comparisons to other methods are carried out in order to verify the performance of the proposed loss probability estimation approach and the efficiency of the admission control scheme in accepting new users to the OFDM/TDMA system.
Protein backbone angle prediction with machine learning approaches

MOTIVATION Protein backbone torsion angle prediction provides useful local structural information that goes beyond conventional three-state (alpha, beta and coil) secondary structure predictions. Accurate prediction of protein backbone torsion angles will substantially improve modeling procedures for local structures of protein sequence segments, especially in modeling loop conformations that do not form regular structures as in alpha-helices or beta-strands. RESULTS We have devised two novel automated methods in protein backbone conformational state prediction: one method is based on support vector machines (SVMs); the other method combines a standard feed-forward back-propagation artificial neural network (NN) with a local structure-based sequence profile database (LSBSP1). Extensive benchmark experiments demonstrate that both methods have improved the prediction accuracy rate over the previously published methods for conformation state prediction when using an alphabet of three or four states. AVAILABILITY LSBSP1 and the NN algorithm have been implemented in PrISM.1, which is available from www.columbia.edu/~ay1/. SUPPLEMENTARY INFORMATION Supplementary data for the SVM method can be downloaded from the Website www.cs. columbia.edu/compbio/backbone.
Beyond Instruction Level Taint Propagation

Dynamic taint analysis (DTA) plays a fundamental role in computer security research. However, current implementations of DTA are often inefficient as taint information is propagated for each instruction. Previous work has suggested propagating taint information at higher abstractions such as functions. But, this has only been achieved by manually instrumenting taint rules for library functions. Research on automatically creating taint propagation rules for higher levels of abstraction is lacking. Towards addressing the research gap, we propose the notion of straight line code units (SLCUs) and describe a technique to reduce higher abstractions like functions to SLCUs. Since a basic block is equivalent to a SLCU, current basic block summarization techniques can be applied to SLCUs. We propose an algorithm for automatically summarizing taint propagations for SLCUs with no or single pointer indirections, which we describe to be unaffected by memory aliasing. Preliminary results indicate that at least 87% of the basic blocks (the most basic form of SLCU) from a set of common Linux libraries fulfill this criteria.
Demanding by Design: Supporting Effortful Communication Practices in Close Personal Relationships

The investment of effort into personal communication can be highly meaningful to people, and has particular significance for the mediation of close relationships. This paper presents qualities of effort investment that are seen to be valuable. Furthermore, we consider how these qualities might sensitise designers of communication technologies to the meaningfulness of effort. We report a qualitative study focusing on individual descriptions of meaningful effort invested into everyday correspondence. We encapsulate our findings in the form of five qualities that characterise valued effort: discretionary investment, personal craft, focused time, responsiveness to the recipient, and challenge to a sender's capacities. Drawing on ideas generated in brainstorming sessions, we present two illustrative concepts for new communication technologies, highlighting how our findings can guide the creation of designed artefacts.
QuickFind: Fast and contact-free object detection using a depth sensor

Pervasive computing applications have long used contact free object detection to process images collected from smartphone, tablet and wearable cameras. Two key challenges encountered in uncontrolled environments are the detection accuracy and speed, more so on computationally limited embedded systems. Recent technological advances have led to the emergence of depth sensors being integrated in a variety of embedded devices such as smartphones and wearables. Depth sensors are contact free and avoid some of the pitfalls caused by variations in lighting and background conditions that are typically associated with images from conventional cameras. This paper presents QuickFind, a fast and lightweight algorithm for object detection using only depth data. QuickFind is fast and particularly suited to run on embedded platforms as it uses a quick method for segmentation and makes use of low overhead features. We demonstrate empirically the performance of QuickFind by benchmarking on two embedded systems: Raspberry Pi and Intel Edison. We also demonstrate the wide applicability of QuickFind by developing two proof-of-concept pervasive computing applications.
Efficiently Exploiting the Context of Object-Action Context for Object Recognition

This research features object recognition that exploits the context of object-action to enhance the recognition performance. We propose an efficient method that integrates human interaction with objects into object recognition using a Bayesian approach based on a simple probabilistic graph model. Experimental results show that our method of using the object-action context is quite effective for object recognition despite of large variation in the appearance of objects.
Implementing the Advanced Switching Minimum Bandwidth Egress Link Scheduler

Advanced switching (AS) is a new fabric-interconnect technology that further enhances the capabilities of PCI Express, which is the next PCI generation. On the other hand, the provision of quality of service (QoS) in computing and communication environments is currently the focus of much discussion and research in industry and academia. One of the mechanisms that AS provides to support QoS is the minimum bandwidth egress link scheduler, or just MinBW scheduler. In this paper, we propose several implementations of the MinBW scheduler and compare their performance by simulation. These implementations fulfill all the properties that an AS MinBW scheduler must have, including the interaction with the AS link layer flow control
Rhetorical video argument analysis

It is documented that video is one of the media used to deliver information, but little is known about rhetorical video and its relation with viewer's behaviors and practices. This study is conducted how behaviors and practices can determine viewer's understanding, based on their facial expression. 14 viewers are selected randomly and their facial expressions are recorded while they are watching the video. Preliminary test shows that 78.6% of the viewers did not know that there are four types of videos, which are; the abstract, associational, categorical and rhetorical videos. This will give the idea that viewer's understanding is important in order to determine and categorize type of video based on their reasoning and feedback.
Bacterial Adhesion: Seen Any Good Biofilms Lately?

SUMMARY The process of surface adhesion and biofilm development is a survival strategy employed by virtually all bacteria and refined over millions of years. This process is designed to anchor microorganisms in a nutritionally advantageous environment and to permit their escape to greener pastures when essential growth factors have been exhausted. Bacterial attachment to a surface can be divided into several distinct phases, including primary and reversible adhesion, secondary and irreversible adhesion, and biofilm formation. Each of these phases is ultimately controlled by the expression of one or more gene products. Ultrastructurally, the mature bacterial biofilm resembles an underwater coral reef containing pyramidal or mushroom-shaped microcolonies of organisms embedded within an extracellular glycocalyx, with channels and cavities to allow the exchange of nutrients and waste. The biofilm protects its inhabitants from predators, dehydration, biocides, and other environmental extremes while regulating population growth and diversity through primitive cell signals. From a physiological standpoint, surface-bound bacteria behave quite differently from their planktonic counterparts. Recognizing that bacteria naturally occur as surface-bound and often polymicrobic communities, the practice of performing antimicrobial susceptibility tests using pure cultures and in a planktonic growth mode should be questioned. That this model does not reflect conditions found in nature might help explain the difficulties encountered in the management and treatment of biomedical implant infections.
High‐resolution calculations of merging neutron stars – II. Neutrino emission

The remnant resulting from the merger of two neutron stars produces neutrinos in copious amounts. In this paper we present the neutrino emission results obtained via Newtonian, high-resolution simulations of the coalescence event. These simulations use three-dimensional smoothed particle hydrodynamics together with a nuclear, temperature-dependent equation of state and a multiflavour neutrino leakage scheme. We present the details of our scheme, discuss the neutrino emission results from a neutron star coalescence and compare them with the core-collapse supernova case where neutrino emission has been studied for several decades. The average neutrino energies are similar to those in the supernova case, but contrary to the latter, the luminosities are dominated by electron-type antineutrinos that are produced in the hot, neutron-rich, thick disc of the merger remnant. The cooler parts of this disc contain substantial fractions of heavy nuclei, which, however, do not influence the overall neutrino emission results significantly. Our total neutrino luminosities from the merger event are considerably lower than those found in previous investigations. This imposes constraints on the ability of neutron star mergers to produce a gamma-ray burst via neutrino annihilation. The neutrinos are emitted preferentially along the initial binary rotation axis, an event seen ‘pole-on’ would appear much brighter in neutrinos than a similar event seen ‘edge-on’.
The Glycan Shield of HIV Is Predominantly Oligomannose Independently of Production System or Viral Clade

The N-linked oligomannose glycans of HIV gp120 are a target for both microbicide and vaccine design. The extent of cross-clade conservation of HIV oligomannose glycans is therefore a critical consideration for the development of HIV prophylaxes. We measured the oligomannose content of virion-associated gp120 from primary virus from PBMCs for a range of viral isolates and showed cross-clade elevation (62–79%) of these glycans relative to recombinant, monomeric gp120 (∼30%). We also confirmed that pseudoviral production systems can give rise to notably elevated gp120 oligomannose levels (∼98%), compared to gp120 derived from a single-plasmid viral system using the HIVLAI backbone (56%). This study highlights differences in glycosylation between virion-associated and recombinant gp120.
Hydrops Fetalis, Cardiovascular Defects, and Embryonic Lethality in Mice Lacking the Calcitonin Receptor-Like Receptor Gene

ABSTRACT Adrenomedullin (AM) is a multifunctional peptide vasodilator that is essential for life. To date, numerous in vitro studies have suggested that AM can mediate its biological effects through at least three different receptors. To determine the in vivo importance of the most likely candidate receptor, calcitonin receptor-like receptor, a gene-targeted knockout model of the gene was generated. Mice heterozygous for the targeted Calcrl allele appear normal, survive to adulthood, and reproduce. However, heterozygote matings fail to produce viable Calcrl −/− pups, demonstrating that Calcrl is essential for survival. Timed matings confirmed that Calcrl −/− embryos die between embryonic day 13.5 (E13.5) and E14.5 of gestation. The Calcrl −/− embryos exhibit extreme hydrops fetalis and cardiovascular defects, including thin vascular smooth muscle walls and small, disorganized hearts remarkably similar to the previously characterized AM −/− phenotype. In vivo assays of cellular proliferation and apoptosis in the hearts and vasculature of Calcrl −/− and AM −/− embryos support the concept that AM signaling is a crucial mediator of cardiovascular development. The Calcrl gene targeted mice provide the first in vivo genetic evidence that CLR functions as an AM receptor during embryonic development.
Evaluating the Quality in the Use of Domain-Specific Languages in an Agile Way

To deal with the increasing complexity of the software systems to be developed, it is important to have high level approaches to development that support such complexity at affordable costs. This fosters the development of Domain-Specific Languages (DSLs) that are claimed to bring important productivity improvements to software developers. Because of that, the quality of the users interaction with this kind of technology is becoming of utmost importance. The goal of this research is to contribute to the systematic activity of software language engineering by focusing on the issue of quality in use evaluation of DSLs, in which design decisions are validated iteratively.