Miracle-dz/UniFAR-FTUs huggingface dataset:
An Effective Sparse Approximate Inverse Preconditioner for Vector Finite Element Analysis of 3D EM Problems

In this paper, we consider a new approach to choose the priori sparsity pattern, and present a pre- and post-filtration technique for sparse approximate inverse (SAI) implementation to alleviate this difficulty. Experiment shows that these tricks are very effective when combined with conjugate gradient (CG) method to solve 3D electromagnetic field (EM) problems
Tyrosine sulfation in the second variable loop (V2) of HIV-1 gp120 stabilizes V2–V3 interaction and modulates neutralization sensitivity

Significance Despite intensive efforts, the structure of the native HIV-1 envelope trimer—the sole relevant target for vaccine design—has remained elusive. Our work identifies a key structural constraint that stabilizes the native envelope conformation and modulates its sensitivity to neutralization. We show that this constraint is established by previously unrecognized sulfated tyrosines within the second variable loop (V2) of the envelope glycoprotein subunit gp120, which mediate intramolecular interaction with the base of the third variable loop, V3. Strikingly, the V2 sulfotyrosines functionally mimic those present in the N terminus of the CCR5 coreceptor, which bind to the same V3 region. Our results shed light on the mechanisms adopted by HIV-1 to elude immunologic control and open new perspectives for vaccine design. Elicitation of broadly neutralizing antibodies is essential for the development of a protective vaccine against HIV-1. However, the native HIV-1 envelope adopts a protected conformation that conceals highly conserved sites of vulnerability from antibody recognition. Although high-definition structures of the monomeric core of the envelope glycoprotein subunit gp120 and, more recently, of a stabilized soluble gp140 trimer have been solved, fundamental aspects related to the conformation and function of the native envelope remain unresolved. Here, we show that the conserved central region of the second variable loop (V2) of gp120 contains sulfated tyrosines (Tys173 and Tys177) that in the CD4-unbound prefusion state mediate intramolecular interaction between V2 and the conserved base of the third variable loop (V3), functionally mimicking sulfated tyrosines in CCR5 and anti–coreceptor-binding-site antibodies such as 412d. Recombinant gp120 expressed in continuous cell lines displays low constitutive levels of V2 tyrosine sulfation, which can be enhanced markedly by overexpression of the tyrosyl sulfotransferase TPST2. In contrast, virion-associated gp120 produced by primary CD4+ T cells is inherently highly sulfated. Consistent with a functional role of the V2 sulfotyrosines, enhancement of tyrosine sulfation decreased binding and neutralization of HIV-1 BaL by monomeric soluble CD4, 412d, and anti-V3 antibodies and increased recognition by the trimer-preferring antibodies PG9, PG16, CH01, and PGT145. Conversely, inhibition of tyrosine sulfation increased sensitivity to soluble CD4, 412d, and anti-V3 antibodies and diminished recognition by trimer-preferring antibodies. These results identify the sulfotyrosine-mediated V2–V3 interaction as a critical constraint that stabilizes the native HIV-1 envelope trimer and modulates its sensitivity to neutralization.
Detecting deceptive engagement in social media by temporal pattern analysis of user behaviors: a survey

Deceptive engagement in social media, such as spamming, commenting, or rating with automatic scripts, spreading fabricated facts, seriously affects users’ trust on online services. Given the large volumes of information generated by users, effectively spotting users involved such deceptive engagement has become a challenging problem. Recent research has shown that techniques for analyzing temporal behavioral patterns are critical to address such problem. In this study, we survey recent advances in these techniques. We first summarize three approaches to model temporal information. Then, by using representative application examples, we discuss recent approaches with respect to their applications to real‐world large‐scale social media. With a focus on the temporal perspective, we then discuss advantages and challenges of each approach. WIREs Data Mining Knowl Discov 2017, 7:e1210. doi: 10.1002/widm.1210
WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures

Summary: The understanding of the biological role of RNA molecules has changed. Although it is widely accepted that RNAs play important regulatory roles without necessarily coding for proteins, the functions of many of these non-coding RNAs are unknown. Thus, determining or modeling the 3D structure of RNA molecules as well as assessing their accuracy and stability has become of great importance for characterizing their functional activity. Here, we introduce a new web application, WebRASP, that uses knowledge-based potentials for scoring RNA structures based on distance-dependent pairwise atomic interactions. This web server allows the users to upload a structure in PDB format, select several options to visualize the structure and calculate the energy profile. The server contains online help, tutorials and links to other related resources. We believe this server will be a useful tool for predicting and assessing the quality of RNA 3D structures. Availability and implementation: The web server is available at http://melolab.org/webrasp. It has been tested on the most popular web browsers and requires Java plugin for Jmol visualization. Contact: fmelo@bio.puc. cl
Disambiguating Levin Verbs Using Untagged Data

Lapata and Brew [8] (hereafter LB04) obtain from untagged texts a statistical prior model that is able to generate class preferences for ambiguous Levin [9] verbs. They also show that their informative priors, incorporated into a Naive Bayesian classifier deduced from handtagged data, can aid in verb class disambiguation. We re-examine the parameter estimation of LB04’s prior model and identify the only parameter in LB04’s prior model that determines the predominant class for a particular verb in a particular frame. In addition, we propose a method for training our classifier without using hand-tagged data. Our experiments suggest that although our verb class disambiguator does not match the performance of the ones that make use of hand-tagged data, it consistently outperforms the random baseline model. Our experiments also demonstrate that the informative priors derived from untagged texts help improve the performance of the classifier trained on untagged data.
A Flexible Translation-Based Knowledge Graph Embedding Adapting Unobserved Entities

This paper proposes a flexible translation-based knowledge graph embedding that learns unobserved entities by moving positions of embedding vectors from existed embedding space. To reflect unobserved entities, previous methods tend to learn knowledge graphs all over again. This process causes high cost of calculation. Thus, this paper introduces an adjusting method which moves positions of learned embedding vectors according to unobserved entity. This idea is based on TransE model that is a one of translation-based methods. According to experiments, the proposed method shows the plausibility at link prediction task and triple classification task. These experimental results prove that reducing learning cost is a crucial issue for embedding knowledge graphs.
Communication in young people with intellectual impairments : the influence of partnership.

Adults with intellectual impairments experience frequent communication breakdown in their everyday interactions. This can result from impairment of the linguistic skills required for effective communication and/or difficulties dealing with non-verbal information. Problems also exist, however, in the way that some non-impaired speakers, such as care providers, approach these communicative episodes. This thesis investigates communication in young adults with intellectual impairments with three different communication partners. These were a care provider, a student and a peer with intellectual impairments. Student partners were previously unknown to the main participants and not experienced in communicating with people with intellectual impairments. Communication structure and process are investigated according to the number of words and turns used to complete a co-operative problem-solving task and the types of conversational acts used by speakers and listeners. Non-verbal communication is investigated through the use of one non-verbal signal, gaze, during the task dialogues. An interactionist approach is taken to communication, where outcome or success is viewed as a product of the collaborative efforts of speakers and listeners. Communication is seen as multi-modal and involving the exchange of information via the verbal and non-verbal channels. The results show that when both parties were intellectually impaired performance was poorest. More surprisingly, dyads including a student partner communicated more effectively and efficiently than where the partner was a carer. One reason for this may be that carers used more complex, open questions to introduce new information into the task, and these were distracting rather than useful. Overusing open questions may be problematic for this population and less effective at establishing shared understanding than where listeners check their own interpretation of previous messages, a strategy preferred by student partners. Non-verbal signals can help to ease constraints on communication by providing interlocutors with feedback information on the levels of mutual understanding.
The potential role of self‐sampling for high‐risk human papillomavirus detection in cervical cancer screening

High‐risk human papillomavirus (hr‐HPV) detection will become an important tool in the screening for cervical cancer. Self‐sampling is an inexpensive and well‐accepted method for HPV detection that will increase participation of nonresponders in current screening programs. Even more, because self‐collected samples are as good as physician‐collected samples for HPV detection, self‐sampling might be a suitable method for future primary cervical cancer screening. Copyright © 2011 John Wiley & Sons, Ltd.
A Randomised, Controlled Clinical Study on Total Hip Arthroplasty Using 4 Different Bearings: Results after 10 Years

Purpose To compare 4 different bearings in total hip arthroplasty (THA) in a randomised controlled clinical study on clinical performance. Methods 393 patients with osteoarthritis of the hip or avascular necrosis were included and allocated to 1 of the head-and-cup couples zirconia-on-polyethylene (group A), metal-on-metal (group B), zirconia-on-polyethylene with the liner moulded into the shell (group C), or alumina-on-alumina (group D). In the individual case the surgeon could choose other implants if indicated. Results 299 patients were operated with the allocated prosthesis. The estimated cumulated prosthesis survival percentages and 95% confidence interval after 10 years were: group A 84.6 (75.8-93.4); group B 95.0 (89.5-100); group C 93.2 (86.7-99.7); group D 66.1 (54.5-77.7). The patients' physical function was significantly improved and remained equally good in all 4 groups, however slightly declining with ageing. The luxation rate was initially high, and equal between the groups, but was reduced by improving the surgical procedure introducing capsule repair by reinsertion of the short external hip rotators. Conclusions The metal-on-metal or zirconia-on-polyethylene prostheses had high 10-year survival percentages. The longevity of these bearing couples by themselves was not related to the combination of materials. The zirconia-on-polyethylene prosthesis with the liner mounted peroperatively possibly exhibited cases of backside wear which the corresponding bearing couple with moulded polyethylene (Asian) did not. The alumina-on-alumina bearing performed poorly - it was redesigned after our study initiation and later withdrawn from the market.
Perceptions of White Men on Affirmative Action Planning

Perceptions of White Men of Affirmative Action Planning by Linda Lee Hansken M.B.A., University of Phoenix, 2002 B.S., Widener University, 1990 Proposal Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Applied Management and Decision Sciences Walden University September 2011
Regional lung ventilation pattern in preschool children with bronchopulmonary dysplasia is modified by bronchodilator response

Bronchopulmonary dysplasia (BPD) remains a significant long‐term complication of prematurity. A standardized method of pulmonary function testing is still not available in preschool children with BPD. We investigated the feasibility of Electrical Impedance Segmentography (EIS) monitoring in this group and the impact of bronchodilator response (BDR) to salbutamol on the pattern of lung ventilation.
Diversity entails improvement: A new neighbour selection scheme for Kademlia-type systems

Discovery of nodes and content in large-scale distributed systems is generally based on Kademlia, today. Understanding Kademlia-type systems to improve their performance is essential for maintaining a high service quality for an increased number of participants, particularly when those systems are adopted by latency-sensitive applications. This paper contributes to the understanding of Kademlia by studying the impact of diversifying neighbours' identifiers within each routing table bucket on the lookup performance. We propose a new, yet backward-compatible, neighbour selection scheme that attempts to maximize the aforementioned diversity. The scheme does not cause additional overhead except negligible computations for comparing the diversity of identifiers. We present a theoretical model for the actual impact of the new scheme on the lookup's hop count and validate it against simulations of three exemplary Kademlia-type systems. We also measure the performance gain enabled by a partial deployment for the scheme in the real KAD system. The results confirm the superiority of the systems that incorporate our scheme.
Warehouse management system in Ruby on Rails framework on cloud computing architecture

This article describes internet-based application for warehouse management written in Ruby with use of Ruby on Rails framework and distributed as Software as a Service (SaaS) platform. This approach allows for great compatibility between operating systems as well as makes it possible to access application from all kind of devices - from standalone desktop computers up to tables and all kind of mobile devices. Example application was developed in Ruby on Rails version 2.3.
Steering Limitations for a Vehicle Pulling Passive Trailers

Motion control of articulated vehicles composed of a nonholonomic tractor and several passive trailers is a difficult underactuated problem. This paper proposes the application of steering limitations to the tractor to avoid inter unit collision during forward motion. This method can be used for systems that combine any type of on-axle and off-axle joints. We propose an algorithm to compute curvature bounds based on the analysis of steady and transient responses. These limitations can be introduced at the path tracking and path planning levels for autonomous navigation. Thus, the tractor can be controlled to follow admissible paths much in the same way as when it does not tow any trailer. The method has been validated experimentally with an off-axle two-trailer setup attached to the tracked mobile robot Auriga-alpha.
Idelalisib Impacts Cell Growth through Inhibiting Translation-Regulatory Mechanisms in Mantle Cell Lymphoma

Purpose: PI3K is a critical node in the B-cell receptor pathway, which is responsible for survival and proliferation of B-cell malignancies. Idelalisib, a PI3Kδ-isoform–specific inhibitor, has been approved to treat B-cell malignancies. Although biological activity of the drug has been evaluated, molecular mechanisms and signaling pathway disruption leading to the biological effects of idelalisib are not yet well defined. Prior laboratory reports have identified transcription and translation as the primary events for attenuation of PI3Kα isoform. We hypothesized that PI3Kδ-isoform inhibition by idelalisib should also affect gene transcription and protein translation. Experimental Design: Using three mantle cell lymphoma cell lines and primary cells from patients, biological consequences such as apoptosis/cell-cycle analysis, as well as RNA/protein synthesis were evaluated. Proteomics analyses (RPPA and immunoblot assays) defined molecular events downstream of PI3K/AKT cassette. Results: Idelalisib treatment resulted in inhibition of protein synthesis, which correlated with reduction in cell size and cell growth. A moderate loss of viability without any change in cell-cycle profile was observed. Idelalisib treatment inhibited AKT activation, an immediate downstream PI3K effector, and also reduced phosphorylation levels of downstream AKT/mTOR pathway proteins such as PRAS40. In addition, idelalisib treatment impeded activation of the MAPK pathway, and MEK, ERK and p90RSK phosphorylation levels were reduced. Reduction in AKT, PDK1, and MEK phosphorylation correlated with protein synthesis inhibition. Conclusions: Collectively, these results clarify the molecular mechanisms of actions and may provide biomarkers and targets for combination with idelalisib in B-cell malignancies. Clin Cancer Res; 23(1); 181–92. ©2016 AACR.
Effect of anti-CD 52 antibody alemtuzumab on ex-vivo culture of umbilical cord blood stem cells

Background: Excessive maturation of hematopoietic cells leads to a reduction of long-term proliferative capability during cord blood (CB) expansion. In this study, we report the effects of anit-CD52 (Alemtuzumab, Campath) on both shortand long-term ex vivo expansion of CB hematopoietic stem cells (HSC) by evaluating the potential role of Alemtuzumab in preserving the repopulating capability in CB HSC and nonlymphoid progenitors. Methods: Ex vivo expansion experiments were carried out using freshly purified CB CD34+ cells in StemSpanTM SFEM medium in the presence of stem cell factor, Flt3-Ligand and thrombopoietin at 50 ng/ml. Alemtuzumab (10 μg/ml) was used to deplete CD52+ cells during the cultures. Flow cytometry was used to monitor CB HSC and their differentiation. Colony forming unit (CFU) assays and long term culture-initiating cell (LTC-IC) assays were performed on cells obtained from day 0 (before culture) and day 14 after cultures. Secondary cultures was performed using CD34+ cells isolated at 35 days from primary cultures and further cultured in StemSpanTM SFEM medium for another 14 days to confirm the long term effect of alemtuzumab in liquid cultures. Results: Compared to cytokines alone, addition of alemtuzumab resulted in a significant increase in total nucleated cells, absolute CD34+ cells, myeloid and megakaryocytic progenitors, multilineage and myeloid CFU and LTC-IC. Conclusion: The results from current study suggested that the use of alemtuzumab for ex vivo expansion of CBHSC maybe advantageous. Our findings may improve current technologies for CBHSC expansion and increase the availability of CB units for transplantation. However, in vivo studies using animal models are likely needed in further studies to test the hematopoietic effects using such expanded CB products. Published: 23 October 2008 Journal of Hematology & Oncology 2008, 1:19 doi:10.1186/1756-8722-1-19 Received: 10 August 2008 Accepted: 23 October 2008 This article is available from: http://www.jhoonline. org/content/1/1/19 © 2008 Lim et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
A network and QoE aware P2P video streaming solution

This paper presents a solution for video streaming in a Peer-to-Peer (P2P) fashion, which takes into account the users' context, including information related to the physical underlying networks (type of access network, topology, Internet Service Provider.), in order to optimize the content delivery. Coupled with this network-aware tree structure, the capability to dynamically adapt video data, by the peers themselves, enable to provide the video in the best possible quality according to the context of the users. Components, launched on the peers, analyse the quality perceived by the end user, namely the QoE (Quality of experience), in real-time in order to reorganize the P2P network in case of insufficient perceived quality. A demonstrator of the solution has been implemented and tests have been done on the PlanetLab network in order to validate the feasibility of such a solution.
Six Honest Serving-Men: Using the Messages of Research to Design Effective Staff Development Programs

Kipling draws a contrast between the appropriate and restrained question-asking of the adult and the indiscriminate and incessant questioning of the young child who "keeps ten million serving men . one million Hows, two million Whens, and seven million Whys! " Adults and children may learn in different ways, yet both adults and children learn in accordance with many of the same basic principles. The basic questions which underlie good curriculum design for children should also underlie curriculum and program-planning for adult educators. The questions are those 4 'servingmen" identified by Kipling:
Shotgun MS proteomic analysis of bronchoalveolar lavage fluid in normal subjects

We provide a review of proteomic techniques used to characterize the bronchoalveolar lavage fluid (BALF) proteome of normal healthy subjects. Bronchoalveolar lavage (BAL) is the most common technique for sampling the components of the alveolar space. The proteomic techniques used to study normal BALF include protein separation by 2DE, whereby proteins were identified by comparison to a reference gel as well as high pressure liquid chromatography (HPLC)‐MS/MS, also known as shotgun proteomics. We summarize recent progress using shotgun MS technologies to define the normal BALF proteome. Surprisingly, we find that despite advances in shotgun proteomic technologies over the course of the last 10 years, which have resulted in greater numbers of proteins being identified, the functional landscape of normal BALF proteome was similarly described by all methods examined.