Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptidoglycan-associated outer membrane protein Mep45 of rumen anaerobe Selenomonas ruminantium forms a non-specific diffusion pore via its C-terminal transmembrane domain

The major outer membrane protein Mep45 of Selenomonas ruminantium, an anaerobic Gram-negative bacterium, comprises two distinct domains: the N-terminal S-layer homologous (SLH) domain that protrudes into the periplasm and binds to peptidoglycan, and the remaining C-terminal transmembrane domain, whose function has been unknown. Here, we solubilized and purified Mep45 and characterized its function using proteoliposomes reconstituted with Mep45. We found that Mep45 forms a nonspecific diffusion channel via its C-terminal region. The channel was permeable to solutes smaller than a molecular weight of roughly 600, and the estimated pore radius was 0.58 nm. Truncation of the SLH domain did not affect the channel property. On the basis of the fact that Mep45 is the most abundant outer membrane protein in S. ruminantium, we conclude that Mep45 serves as a main pathway through which small solutes diffuse across the outer membrane of this bacterium. Graphical abstract Schematic representation of Mep45 in the outer membrane of S. ruminantium. The C-terminal region of Mep45 forms a non-specific diffusion channel.
Overview of NTCIR-9

This is an overview of NTCIR-9, the Ninth NTCIR Workshop. It touches upon a brief history of NTCIR, introduces the tasks run at NTCIR-9, and reports on some statistics across these tasks. For details on the individual tasks, we refer the reader to the task overview papers and the participants’ papers.
A mechanism for biologically-induced iodine emissions from sea-ice

A mechanism for biologically-induced iodine emissions from sea-ice A. Saiz-Lopez and C. S. Boxe Earth and Space Science Division, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA Received: 2 January 2008 – Accepted: 7 January 2008 – Published: 13 February 2008 Correspondence to: A. Saiz-Lopez (alfonso.saiz-lopez@jpl.nasa.gov) Published by Copernicus Publications on behalf of the European Geosciences Union.
Modelling and Control of a Worm-Like Micro Robot with Active Force Control Capability

In this paper, a pneumatic worm-like micro robot with active force control (AFC) capability is modelled and simulated in a constrained environment (pipe). A mathematical model that represents the dynamic characteristics of the worm-like micro robot is first presented. Then, the dynamic response of the robot system subjected to different input excitations is investigated. A proportional-integral-derivative (PID) controller is applied to the micro robot system to follow the desired trajectory while an AFC controller is utilized to reject the unwanted disturbances which may be created due to frictional forces or fluid viscosity in the pipe. The control system is tuned so that an accurate trajectory tracking is possible. The performance of the control system under different types of disturbances is evaluated through a rigorous simulation study. The obtained results clearly demonstrate an effective trajectory tracking capability of the worm-like micro robot in spite of the negative effects of the external disturbances.
Understanding the role of embarrassment in gynaecological screening: a qualitative study from the ASPIRE cervical cancer screening project in Uganda

Objective To define embarrassment and develop an understanding of the role of embarrassment in relation to cervical cancer screening and self-collected human papillomavirus (HPV) DNA testing in Uganda. Design Cross-sectional, qualitative study using semistructured one-to-one interviews and focus groups. Participants 6 key-informant health workers and 16 local women, purposively sampled. Key informant inclusion criteria: Ugandan members of the project team. Focus group inclusion criteria: woman age 30–69 years, Luganda or Swahili speaking, living or working in the target Ugandan community. Exclusion criteria: unwillingness to sign informed consent. Setting Primary and tertiary low-resource setting in Kampala, Uganda. Results In Luganda, embarrassment relating to cervical cancer is described in two forms. ‘Community embarrassment’ describes discomfort based on how a person may be perceived by others. ‘Personal embarrassment’ relates to shyness or discomfort with her own genitalia. Community embarrassment was described in themes relating to place of study recruitment, amount of privacy in dwellings, personal relationship with health workers, handling of the vaginal swab and misunderstanding of HPV self-collection as HIV testing. Themes of personal embarrassment related to lack of knowledge, age and novelty of the self-collection swab. Overall, embarrassment was a barrier to screening at the outset and diminished over time through education and knowledge. Fatalism regarding cervical cancer diagnosis, worry about results and stigma associated with a cervical cancer diagnosis were other psychosocial barriers described. Overcoming psychosocial barriers to screening can include peer-to-peer education, drama and media campaigns. Conclusions Embarrassment and other psychosocial barriers may play a large role at the onset of a screening programme, but over time as education and knowledge increase, and the social norms around screening evolve, its role diminishes. The role of peer-to-peer education and community authorities on healthcare cannot be overlooked and can have a major impact in overcoming psychosocial and social barriers to screening.
Delineating Psychopathy from Cognitive Empathy

There is an ongoing debate regarding the content of psychopathy, especially about the status of antisocial behavior and disinhibition characteristics as core psychopathy features. Psychopathic Personality Traits Scale (PPTS) represents a novel model of psychopathy based on core psychopathy markers such as Interpersonal manipulation, Egocentricity and Affective responsiveness. However, this model presupposes another narrow trait of psychopathy: cognitive responsiveness, which represents a lack of cognitive empathy. Since previous models of psychopathy do not depict this feature as a core psychopathy trait, the goal of this study was to empirically evaluate if the lack of cognitive empathy is a narrow psychopathy trait or its correlate. The research was conducted on a community sample via online study (N=342; Mage=23.7 years; 31% males). Results showed that the correlations between Cognitive responsiveness and other psychopathy features were significantly lower than intercorrelations of other three traits. Factor analysis, conducted on PPTS items, provided a two-factor solution, where Cognitive responsiveness was yielded as a factor separate from other psychopathy indicators. Finally, the exploration of the shared latent space of psychopathy and cognitive empathy resulted in the two-factor solution where psychopathy and the lack of cognitive empathy were extracted as correlated but separate latent variables. The data clearly supported the former model. Research results showed that the lack of cognitive empathy should not be considered an indicator of psychopathy but its correlate. The findings emphasize the need to be cautious in conceptualization of the psychopathy construct.
Engineering of the Dsb (disulfide bond) proteins – contribution towards understanding their mechanism of action and their applications in biotechnology and medicine

Abstract The Dsb protein family in prokaryotes catalyzes the generation of disulfide bonds between thiol groups of cysteine residues in nascent proteins, ensuring their proper three-dimensional structure; these bonds are crucial for protein stability and function. The first Dsb protein, Escherichia coli DsbA, was described in 1991. Since then, many details of the bond-formation process have been described through microbiological, biochemical, biophysical and bioinformatics strategies. Research with the model microorganism E. coli and many other bacterial species revealed an enormous diversity of bond-formation mechanisms. Research using Dsb protein engineering has significantly helped to reveal details of the disulfide bond formation. The first part of this review presents the research that led to understanding the mechanism of action of DsbA proteins, which directly transfer their own disulfide into target proteins. The second part concentrates on the mechanism of electron transport through the cell cytoplasmic membrane. Third and lastly, the review discusses the contribution of this research towards new antibacterial agents.
Controlled vocabulary based software requirements classification

The nature of software requirements is very much subjective and multi-faceted. The level of complexity increases along-with the volume, especially when the requirements are in natural language. In the primary phase of requirements engineering, it is mostly desirable to transform these user written requirements into more understandable form. Organizing the requirements in different groups may support further activities much easier than direct working. In this paper, we present a classifier that sufficiently transforms natural language written requirements into corresponding groups. The organization of these groups depends upon the inter-keywords association i.e., hierarchy of keywords. The classifier works best when requirements have been written using relative vocabulary i.e., controlled vocabulary. The overall structure of this technique is composed on three main components: 1) Repository: of keywords and their relationships as source data, 2) Mapping: Finding words in the requirements document with keywords of repository, and 3) Presentation: presenting classified (grouped) requirements in more meaningful ways.
Meeting Review: ESF Workshop on ‘Impact of Nucleic Acid Chemistry on Gene Function Analysis: Antisense, Aptamers, Ribozymes and RNAi’

The shortage of functional information compared to the abundance of sequence information characterizes today’s situation in functional genomics. For many years the knock-down of a gene’s product has been the most powerful way of analysing its function. In addition to the complete knock-out by homologous recombination, several different techniques have been developed to temporarily knock down gene expression through methods based on specific sequence recognition, such as knockdown by antisense oligonucleotides, ribozymes, aptamers or RNAi. The ESF workshop on ‘Impact of Nucleic Acid Chemistry on Gene Function Analysis’ brought together researchers who use techniques that are different but highly related. It offered an opportunity for an in-depth discussion of recent progress and common problems. Antisense oligonucleotides, aptamers and ribozymes are techniques that have been used successfully for many years to validate targets. However, recent developments, such as increased tightness of binding (e.g. locked nucleic acids) or the combination of different methods (e.g. using aptamers to design ribozymes), have continued to improve the existing techniques. RNA interference (RNAi) is a defence mechanism of the cell against viruses. Since the exact mechanism of action within the cell is still unclear, RNAi was a particularly exciting topic at the workshop and was addressed in the largest number of presentations. Predictability of positional effects (accessibility of RNA) is a problem shared by all techniques using sequence-specific recognition and was the subject of quite controversial debates. The meeting comprised over 50 people from 14 countries (13 European countries and the USA).
Building Cuthbert Hall Vitual College as a Dramatically Engaging Environment

This paper outlines the interdisciplinary nature, collaborative work patterns and role of aesthetics in the Cuthbert Hall Virtual College research project at the Cambridge University Moving Image Studio (CUMIS) and the Centre for Applied Research in Education Technology (CARET). The project identifies key properties of dramatically engaging real-time three-dimensional virtual environments (RT 3D VE) and how the holistic experiential phenomenon of place is organised and mediated through spatial narrative patterns. Interdisciplinary by nature, the project requires a collaborative approach between science, engineering, media and architecture, and the results are revealing for all these areas. The Cuthbert Hall project invites discussion of the importance in the creation and use of RT 3D VE's - under single and multi-user conditions - of articulate aesthetics (the quality of architectural, visual and audio design; the production and incorporation of dramatic properties) and of the conditions required for collaborative, communicative use ofthe environment. The full theoretical and technical discussions as well as the evaluation results are outside the scope of this submission.
IMAGING THE CIRCUMNUCLEAR REGION OF NGC 1365 WITH CHANDRA

We present the first Chandra/ACIS imaging study of the circumnuclear region of the nearby Seyfert galaxy NGC 1365. The X-ray emission is resolved into pointlike sources and complex, extended emission. The X-ray morphology of the extended emission shows a biconical soft X-ray-emission region extending ∼5 kpc in projection from the nucleus, coincident with the high-excitation outflow cones seen in optical emission lines particularly to the northwest. Harder X-ray emission is detected from a kpc-diameter circumnuclear ring, coincident with the star-forming ring prominent in the Spitzer mid-infrared (IR) images; this X-ray emission is partially obscured by the central dust lane of NGC 1365. Spectral fitting of spatially separated components indicates a thermal plasma origin for the soft extended X-ray emission (kT = 0.57 keV). Only a small amount of this emission can be due to photoionization by the nuclear source. Detailed comparison with [O iii]λ5007 observations shows that the hot interstellar medium (ISM) is spatially anticorrelated with the [O iii]-emitting clouds and has thermal pressures comparable to those of the [O iii] media, suggesting that the hot ISM acts as a confining medium for the cooler photoionized clouds. The abundance ratios of the hot ISM are fully consistent with the theoretical values for enrichment from Type II supernovae, suggesting that the hot ISM is a wind from the starburst circumnuclear ring. X-ray emission from a ∼450 pc long nuclear radio jet is also detected to the southeast.
Localized bi-Laplacian Solver on a Triangle Mesh and Its Applications

Partial differential equations(PDE) defined over a surface are used in various graphics applications, such as mesh fairing, smoothing, surface editing, and simulation. Often these applications involve PDEs with Laplacian or bi-Laplacian terms. We propose a new approach to a finite element method for solving these PDEs that works directly on the triangle mesh connectivity graph that has more connectivity information than the sparse matrix. Thanks to these extra information in the triangle mesh, the solver can be restricted to operate on a sub-domain, which is a portion of the surface defined by user or automatically self-adjusting. Our formulation permits us to solve high order terms such as bi-Laplacian by using a simple linear triangle element. We demonstrate the benefits of our approach on two applications: scattered data interpolation over a triangle mesh(painting), and haptic interaction with a deformable surface.
RNA-Directed Therapy: The Next Step in the miRNA Revolution.

RNA, once regarded as merely a messenger molecule in the process of gene expression, has recently emerged as a promising target for cancer therapy (reviewed in [1]). A major role for RNA in eukaryotes is carrying a DNA message from the cell nucleus to the cytoplasm, where it provides a template for protein synthesis. However, the recent discovery of small RNAs or microRNAs (miRNAs) that regulate the function and stability of messenger RNAs (mRNAs) has provided new roles for RNA regulating cell processes. Additionally, small RNAs are being exploited as a tool in systems biology to understand gene regulatory networks. We have just returned from a Forbeck Foundation Forum (http://www.wgfrf.org), held annually in Hilton Head Island, South Carolina, at which 16 leaders in the miRNA field talked about their latest work. Theirs is a message that deserves the widest circulation, for it portends a major change in our concepts of the origins, diagnosis, and treatment of cancer. These small RNAs may prove “imperial” like the diminutive Napoleon Bonaparte who was also short . but mighty. Instructions for about 20,000 protein-coding genes are contained in the DNA sequence of the human genome. mRNAs are strands of hundreds to thousands of nucleotides that serve as templates for synthesis of proteins by ribosomes found in the cytoplasm. Translation into proteins may be affected by several factors, including amino acid availability, the levels of specific proteins involved in translation, and feedback effects of the coded proteins. Regulation of translation has mainly been ascribed to interactions between proteins and the noncoding portions of the mRNA itself. It has generally been thought that these proteins were solely responsible for control of translation. Now, evidence is mounting that miRNAs bind to these noncoding regions of mRNA and exert profound effects on protein synthesis and consequently cell functions. The implications for cancer are astonishing. First discovered 14 years ago in Caenorhabditis elegans [2, 3], a primitive worm, miRNAs may target at least one third of all mRNAs. On average, each of the approximately 600 miRNAs found in mammalian cells contains partial sequence homology to 100–200 mRNAs. miRNAs have been implicated in the regulation of a diversity of processes, such as Band T-cell development, antigen response, immune surveillance and tolerance, and other basic functions such as cell proliferation and death. In distinction to artificially synthesized small interfering RNAs, which target a single mRNA and cause its digestion by endonucleases, miRNAs target multiple mRNAs through partial sequence complementarity and function primarily by inhibiting protein translation (Fig. 1). However, new work by a Yale team has added a new dimension, suggesting that, in synchronously replicating cells, miRNAs may reverse course and become stimulatory to RNA translation [4]. Recent work from several laboratories has revealed that, in the development of lymphoid cells from undifferentiated precursors to mature antigen responders, specific miRNAs
Some Fuzzy Logic Based Congestion Control Methods : A Review

Congestion is the problem that occurs due to saturation of network resources. Despite the implementation of traditional congestion control algorithms such as Transmission Control Protocol (TCP/IP), congestion remains a critical issue in computer and ATM networks. Fuzzy Logic is applied to solve the congestion control problem as communication networks are difficult to model using traditional control system theory. Fuzzy Logic Systems are model free systems that rely on expert knowledge to generate control decision. Fuzzy Logic based congestion control outperforms the traditional methods in several cases . This paper is a review of Fuzzy Logic and Neural-Fuzzy based techniques that are applied to deal with congestion. Fuzzy Logic based Congestion Controller is a model free controller that utilizes qualitative reasoning to implement non-linear control functions efficiently.
Beyond risk and vulnerability: a commentary on “TB, staring, love and loneliness: Flavia’s story”

This article comments on the photo essay “TB, Staring, Love and Loneliness: Flavia’s Story” by Pieter du Plessis, Siv Tshefu and Flavia Nazier, published in the same issue. It contextualizes the essay and Flavia’s story against the historical and contemporary relationship between medicine and gender diversity to emphasise the essay’s argument about agency and resilience.
Pre-Touch Sensing for Mobile Interaction

Touchscreens continue to advance including progress towards sensing fingers proximal to the display. We explore this emerging pre-touch modality via a self-capacitance touchscreen that can sense multiple fingers above a mobile device, as well as grip around the screen's edges. This capability opens up many possibilities for mobile interaction. For example, using pre-touch in an anticipatory role affords an "ad-lib interface" that fades in a different UI--appropriate to the context--as the user approaches one-handed with a thumb, two-handed with an index finger, or even with a pinch or two thumbs. Or we can interpret pre-touch in a retroactive manner that leverages the approach trajectory to discern whether the user made contact with a ballistic vs. a finely-targeted motion. Pre-touch also enables hybrid touch + hover gestures, such as selecting an icon with the thumb while bringing a second finger into range to invoke a context menu at a convenient location. Collectively these techniques illustrate how pre-touch sensing offers an intriguing new back-channel for mobile interaction.
Extending Program Slicing in Aspect-Oriented Programming with InterType Declarations

Program slicing can be very useful for understanding and debugging aspect-oriented programs. Program slicing is a common technique, but it is not trivial to use in aspectoriented programming. Current implementations of slicing tools lack support for features of popular aspect-oriented languages. This paper proposes a detailed algorithm for the construction of an aspect-oriented system dependence graph, with support for inter-type declarations. Known algorithms can then calculate a program slice based on a dependence graph.
Framework for selecting an appropriate e-business model in managerial holding companies: Case study: Iran Khodro

Purpose – The main aim of the present study is to propose a framework for selecting an appropriate electronic business (e‐business) model in managerial holding companies with a chain structure acting in the area of the automobile industry.Design/methodology/approach – This is an applied study conducted as a survey and case study. First, the factors affecting selection of an appropriate e‐business model in managerial holding companies with chain structure in auto industry are identified through a survey and by testing hypotheses. Then, these factors are measured as a case study in Iran Khodro Co. so that the appropriate e‐business model can be determined for this managerial holding company with chain structure.Findings – In this study, 18 different factors were identified for the five main criteria in identifying e‐business. Using the survey conducted in the statistical sample, only three factors of internal and external integration of human resources, flexibility, and decentralization in the responsibilit.
A Look-Ahead Approach to Secure Multiparty Protocols

Secure multiparty protocols have been proposed to enable noncolluding parties to cooperate without a trusted server. Even though such protocols prevent information disclosure other than the objective function, they are quite costly in computation and communication. The high overhead motivates parties to estimate the utility that can be achieved as a result of the protocol beforehand. In this paper, we propose a look-ahead approach, specifically for secure multiparty protocols to achieve distributed k-anonymity, which helps parties to decide if the utility benefit from the protocol is within an acceptable range before initiating the protocol. The look-ahead operation is highly localized and its accuracy depends on the amount of information the parties are willing to share. Experimental results show the effectiveness of the proposed methods.